SERVERCNTRL/Makefile

+# for variables passed from parent makefile see ../SOURCE_TOOLS/parent_make.txt
+.SUFFIXES: .o .c .cxx .depend
+OBJECTS = servercntrl.o
+$(MAIN): $(OBJECTS)
+	$(LINK_STATIC_LIB) $(@) $(OBJECTS)
+.c.o:
+	$(A_CC) $(cflags) -c $< $(CC_INCLUDES) $(POST_COMPILE)
+.cxx.o:
+	$(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
+
+proto:
+	../AISC_MKPTPS/aisc_mkpt -P -w servercntrl.h $(OBJECTS:.o=.cxx) >servercntrl.h.tmp
+	../SOURCE_TOOLS/mv_if_diff servercntrl.h.tmp servercntrl.h
+
+clean:
+	rm -f $(OBJECTS) *.a
+
+DEPENDS = $(OBJECTS:.o=.depend)
+depends: $(DEPENDS)
+	@cat $(DEPENDS) | grep -v '^#' >>Makefile
+	@rm $(DEPENDS)
+$(DEPENDS): depend.init
+depend.init:
+	$(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
+.c.depend:
+	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
+.cxx.depend:
+	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
+
+# DO NOT DELETE THIS LINE -- make depend depends on it.
+
+# Do not add dependencies manually - use 'make depend' in $ARBHOME
+# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from main)
+
+servercntrl.o: servercntrl.h
+servercntrl.o: $(ARBHOME)/INCLUDE/ad_prot.h
+servercntrl.o: $(ARBHOME)/INCLUDE/aisc_global.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arb_assert.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arb_core.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arb_error.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arb_file.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arb_msg.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arb_sleep.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arb_string.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arbdb.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arbdb_base.h
+servercntrl.o: $(ARBHOME)/INCLUDE/arbtools.h
+servercntrl.o: $(ARBHOME)/INCLUDE/attributes.h
+servercntrl.o: $(ARBHOME)/INCLUDE/bytestring.h
+servercntrl.o: $(ARBHOME)/INCLUDE/client.h
+servercntrl.o: $(ARBHOME)/INCLUDE/client_privat.h
+servercntrl.o: $(ARBHOME)/INCLUDE/client_types.h
+servercntrl.o: $(ARBHOME)/INCLUDE/cxxforward.h
+servercntrl.o: $(ARBHOME)/INCLUDE/dupstr.h
+servercntrl.o: $(ARBHOME)/INCLUDE/gccver.h
+servercntrl.o: $(ARBHOME)/INCLUDE/SigHandler.h
+servercntrl.o: $(ARBHOME)/INCLUDE/smartptr.h
+servercntrl.o: $(ARBHOME)/INCLUDE/test_global.h
+servercntrl.o: $(ARBHOME)/INCLUDE/ut_valgrinded.h

SERVERCNTRL/needs_libs

+# libraries needed to link against SERVERCNTRL/SERVERCNTRL.a
+
+lib/libARBDB.so
+
+# it does not matter which client.a is linked
+# (e.g. arb_ntree only links PROBE_COM/client.a, so we always use that one)
+PROBE_COM/client.a
+

SERVERCNTRL/servercntrl.cxx

+// ============================================================= //
+//                                                               //
+//   File      : servercntrl.cxx                                 //
+//   Purpose   :                                                 //
+//                                                               //
+//   Institute of Microbiology (Technical University Munich)     //
+//   http://www.arb-home.de/                                     //
+//                                                               //
+// ============================================================= //
+
+#include <servercntrl.h>
+
+#include <client_privat.h>
+#include <client.h>
+
+#include <arbdb.h>
+#include <arb_file.h>
+#include <arb_sleep.h>
+#include <ut_valgrinded.h>
+
+/* The following lines go to servercntrl.h
+ * edit here, not there!!
+ * call 'make proto' to update
+ */
+
+// AISC_MKPT_PROMOTE:#ifndef ARBDB_BASE_H
+// AISC_MKPT_PROMOTE:#include <arbdb_base.h>
+// AISC_MKPT_PROMOTE:#endif
+// AISC_MKPT_PROMOTE:
+// AISC_MKPT_PROMOTE:struct arb_params {
+// AISC_MKPT_PROMOTE:    char *species_name;
+// AISC_MKPT_PROMOTE:    char *extended_name;
+// AISC_MKPT_PROMOTE:    char *alignment;
+// AISC_MKPT_PROMOTE:    char *default_file;
+// AISC_MKPT_PROMOTE:    char *field;
+// AISC_MKPT_PROMOTE:    const char *field_default;
+// AISC_MKPT_PROMOTE:
+// AISC_MKPT_PROMOTE:    int  read_only;
+// AISC_MKPT_PROMOTE:
+// AISC_MKPT_PROMOTE:    char *job_server;
+// AISC_MKPT_PROMOTE:    char *db_server;
+// AISC_MKPT_PROMOTE:    char *mgr_server;
+// AISC_MKPT_PROMOTE:    char *pt_server;
+// AISC_MKPT_PROMOTE:
+// AISC_MKPT_PROMOTE:    char *tcp;
+// AISC_MKPT_PROMOTE:};
+
+#define TRIES 1
+
+static struct gl_struct {
+    aisc_com   *link;
+    AISC_Object  com;
+
+    gl_struct()
+        : link(0), com(0x10000*1) // faked type id (matches main object)
+    { }
+} glservercntrl;
+
+
+char *prefixSSH(const char *host, const char *command, int async) {
+    /* 'host' is a hostname or 'hostname:port' (where hostname may be an IP)
+       'command' is the command to be executed
+       if 'async' is 1 -> append '&'
+
+       returns a SSH system call for foreign host or
+       a direct system call for the local machine
+    */
+
+    char *result    = 0;
+    char  asyncChar = " &"[!!async];
+
+    if (host && host[0]) {
+        const char *hostPort = strchr(host, ':');
+        char       *hostOnly = GB_strpartdup(host, hostPort ? hostPort-1 : 0);
+
+        if (!GB_host_is_local(hostOnly)) {
+            result = GBS_global_string_copy("ssh %s -n '%s' %c", hostOnly, command, asyncChar);
+        }
+        free(hostOnly);
+    }
+
+    if (!result) {
+        result = GBS_global_string_copy("(%s) %c", command, asyncChar);
+    }
+
+    return result;
+}
+
+GB_ERROR arb_start_server(const char *arb_tcp_env, int do_sleep)
+{
+    const char *tcp_id;
+    GB_ERROR    error = 0;
+
+    if (!(tcp_id = GBS_read_arb_tcp(arb_tcp_env))) {
+        error = GB_export_errorf("Entry '%s' in $(ARBHOME)/lib/arb_tcp.dat not found", arb_tcp_env);
+    }
+    else {
+        const char *server       = strchr(tcp_id, 0) + 1;
+        char       *serverparams = 0;
+
+        /* concatenate all params behind server
+           Note :  changed behavior on 2007/Mar/09 -- ralf
+           serverparams now is one space if nothing defined in arb_tcp.dat
+           (previously was same as 'server' - most likely a bug)
+        */
+        {
+            const char *param  = strchr(server, 0)+1;
+            size_t      plen   = strlen(param);
+            size_t      alllen = 0;
+
+            while (plen) {
+                param  += plen+1;
+                alllen += plen+1;
+                plen    = strlen(param);
+            }
+
+            serverparams = (char*)malloc(alllen+1);
+            {
+                char *sp = serverparams;
+
+                param = strchr(server, 0)+1;
+                plen  = strlen(param);
+                if (!plen) sp++;
+                else do {
+                    memcpy(sp, param, plen);
+                    sp[plen]  = ' ';
+                    sp       += plen+1;
+                    param    += plen+1;
+                    plen      = strlen(param);
+                } while (plen);
+                sp[-1] = 0;
+            }
+        }
+
+        {
+            char *command = 0;
+
+            if (*tcp_id == ':') { // local mode
+                command = GBS_global_string_copy("%s %s -T%s &", server, serverparams, tcp_id);
+                make_valgrinded_call(command);
+            }
+            else {
+                const char *port = strchr(tcp_id, ':');
+
+                if (!port) {
+                    error = GB_export_errorf("Error: Missing ':' in line '%s' file $(ARBHOME)/lib/arb_tcp.dat", arb_tcp_env);
+                }
+                else {
+                    char *remoteCommand = GBS_global_string_copy("$ARBHOME/bin/%s %s -T%s", server, serverparams, port);
+                    make_valgrinded_call(remoteCommand);
+                    command = prefixSSH(tcp_id, remoteCommand, 1);
+                    free(remoteCommand);
+                }
+            }
+
+            if (!error) {
+                error = GBK_system(command);
+                if (do_sleep) GB_sleep(5, SEC);
+            }
+            free(command);
+        }
+        free(serverparams);
+    }
+    return error;
+}
+
+static GB_ERROR arb_wait_for_server(const char *arb_tcp_env, const char *tcp_id, int magic_number, struct gl_struct *serverctrl, int wait) {
+    GB_ERROR error   = NULL;
+    serverctrl->link = aisc_open(tcp_id, serverctrl->com, magic_number, &error);
+
+    if (!error && !serverctrl->link) { // no server running -> start one
+        error = arb_start_server(arb_tcp_env, 0);
+        while (!error && !serverctrl->link && wait) {
+            GB_sleep(1, SEC);
+            wait--;
+            if ((wait%10) == 0 && wait>0) {
+                printf("Waiting for server '%s' to come up (%i seconds left)\n", arb_tcp_env, wait);
+            }
+            serverctrl->link  = aisc_open(tcp_id, serverctrl->com, magic_number, &error);
+        }
+    }
+
+    return error;
+}
+
+GB_ERROR arb_look_and_start_server(long magic_number, const char *arb_tcp_env) {
+    GB_ERROR    error       = 0;
+    const char *tcp_id      = GBS_read_arb_tcp(arb_tcp_env);
+    const char *arb_tcp_dat = "$(ARBHOME)/lib/arb_tcp.dat";
+
+    if (!tcp_id) {
+        error = GBS_global_string("Entry '%s' not found in %s", arb_tcp_env, arb_tcp_dat);
+    }
+    else {
+        const char *file = GBS_scan_arb_tcp_param(tcp_id, "-d"); // find parameter behind '-d'
+
+        if (!file) {
+            error = GBS_global_string("Parameter -d missing for entry '%s' in %s", arb_tcp_env, arb_tcp_dat);
+        }
+        else {
+            if (strcmp(file, "!ASSUME_RUNNING") == 0) {
+                // assume pt-server is running on a host,  w/o access to common network drive
+                // i.e. we cannot check for the existence of the database file
+            }
+            else if (GB_size_of_file(file) <= 0) {
+                if (strncmp(arb_tcp_env, "ARB_NAME_SERVER", 15) == 0) {
+                    char *dir       = strdup(file);
+                    char *lastSlash = strrchr(dir, '/');
+
+                    if (lastSlash) {
+                        lastSlash[0]         = 0; // cut off file
+                        {
+                            const char *copy_cmd = GBS_global_string("cp %s/names.dat.template %s", dir, file);
+                            error                = GBK_system(copy_cmd);
+                        }
+                        if (!error && GB_size_of_file(file) <= 0) {
+                            error = GBS_global_string("Cannot copy nameserver template (%s/names.dat.template missing?)", dir);
+                        }
+                    }
+                    else {
+                        error = GBS_global_string("Can't determine directory from '%s'", dir);
+                    }
+                    free(dir);
+                }
+                else if (strncmp(arb_tcp_env, "ARB_PT_SERVER", 13) == 0) {
+                    const char *nameOnly    = strrchr(file, '/');
+                    if (!nameOnly) nameOnly = file;
+
+                    error = GBS_global_string("PT_server '%s' has not been created yet.\n"
+                                              " To create it follow these steps:\n"
+                                              " 1. Start ARB on the whole database you want to use for probe match/design\n"
+                                              " 2. Go to ARB_NTREE/Probes/PT_SERVER Admin\n"
+                                              " 3. Select '%s' and press BUILD SERVER\n"
+                                              " 4. Wait (up to hours, depending on your DB size)\n"
+                                              " 5. Meanwhile read the help file: PT_SERVER: What Why and How",
+                                              file, nameOnly);
+                }
+                else {
+                    error = GBS_global_string("The file '%s' is missing. \nUnable to start %s", file, arb_tcp_env);
+                }
+            }
+        }
+
+        if (!error) {
+            error = arb_wait_for_server(arb_tcp_env, tcp_id, magic_number, &glservercntrl, 20);
+
+            if (!error) {
+                if (!glservercntrl.link) { // couldn't start server
+                    error =                                                            // |
+                        "ARB has problems to start a server! Possible reasons may be one\n"
+                        "or several of the following list:\n"
+                        "- the tcp_id (socket number) is already used by another program\n"
+                        "  (doesnt apply to user-specific PTSERVERs; check $ARBHOME/lib/arb_tcp.dat versus /etc/services)\n"
+                        "- the server exited with error or has crashed.\n"
+                        "  In case of PTSERVER, the failure might be caused by:\n"
+                        "  - missing database in $ARBHOME/lib/pts/* (solution: update ptserver database)\n"
+                        "  - wrong permissions of $ARBHOME/lib/pts/* (no read access)\n"
+                        "  If you recently installed a new arb version, arb will continue\n"
+                        "  to use your previous 'arb_tcp.dat', which might be out-of-date.\n"
+                        "  Backup and remove it, then restart ARB. If it works now,\n"
+                        "  compare your old 'arb_tcp.dat' with the new one for changes.\n"
+                        "- When using remote servers: login or network problems\n"
+                        ;
+                }
+                else {
+                    aisc_close(glservercntrl.link, glservercntrl.com);
+                    glservercntrl.link = 0;
+                }
+            }
+        }
+    }
+
+    return error;
+}
+
+GB_ERROR arb_look_and_kill_server(int magic_number, const char *arb_tcp_env) {
+    const char *tcp_id;
+    GB_ERROR    error = 0;
+
+    if (!(tcp_id = GBS_read_arb_tcp(arb_tcp_env))) {
+        error = GB_export_errorf("Missing line '%s' in $(ARBHOME)/lib/arb_tcp.dat:", arb_tcp_env);
+    }
+    else {
+        const char *server = strchr(tcp_id, 0)+1;
+
+        glservercntrl.link = aisc_open(tcp_id, glservercntrl.com, magic_number, &error);
+        if (glservercntrl.link) {
+            aisc_close(glservercntrl.link, glservercntrl.com);
+            glservercntrl.link = 0;
+
+            const char *command = GBS_global_string("%s -kill -T%s &", server, tcp_id);
+            if (system(command) != 0) {
+                error = GBS_global_string("Failed to execute '%s'", command);
+            }
+        }
+        else {
+            error = "Server is not running";
+        }
+    }
+    return error;
+}
+
+void arb_print_server_params() {
+    printf("General server parameters (some maybe unused by this server):\n"
+           "    -s<name>        sets species name to '<name>'\n"
+           "    -e<name>        sets extended name to '<name>'\n"
+           "    -a<ali>         sets alignment to '<ali>'\n"
+           "    -d<file>        sets default file to '<file>'\n"
+           "    -f<field>=<def> sets DB field to '<field>' (using <def> as default)\n"
+           "    -r              read-only mode\n"
+           "    -D<server>      sets DB-server to '<server>'  [default = ':']\n"
+           "    -J<server>      sets job-server to '<server>' [default = 'ARB_JOB_SERVER']\n"
+           "    -M<server>      sets MGR-server to '<server>' [default = 'ARB_MGR_SERVER']\n"
+           "    -P<server>      sets PT-server to '<server>'  [default = 'ARB_PT_SERVER']\n"
+           "    -T<[host]:port>   sets TCP connection to '<[host]:port>'\n"
+           );
+}
+
+arb_params *arb_trace_argv(int *argc, const char **argv)
+{
+    int s, d;
+
+    arb_params *erg = (arb_params *)calloc(sizeof(arb_params), 1);
+    erg->db_server  = strdup(":");
+    erg->job_server = strdup("ARB_JOB_SERVER");
+    erg->mgr_server = strdup("ARB_MGR_SERVER");
+    erg->pt_server  = strdup("ARB_PT_SERVER");
+
+    for (s=d=0; s<*argc; s++) {
+        if (argv[s][0] == '-') {
+            switch (argv[s][1]) {
+                case 's': erg->species_name  = strdup(argv[s]+2); break;
+                case 'e': erg->extended_name = strdup(argv[s]+2); break;
+                case 'a': erg->alignment     = strdup(argv[s]+2); break;
+                case 'd': erg->default_file  = strdup(argv[s]+2); break;
+                case 'f': {
+                    char *eq;
+                    erg->field = strdup(argv[s]+2);
+
+                    eq = strchr(erg->field, '=');
+                    if (eq) {
+                        erg->field_default = eq+1;
+                        eq[0]              = 0;
+                    }
+                    else {
+                        erg->field_default = 0; // this is illegal - error handling done in caller
+                    }
+                    break;
+                }
+                case 'r': erg->read_only     = 1; break;
+                case 'J': freedup(erg->job_server, argv[s]+2); break;
+                case 'D': freedup(erg->db_server, argv[s]+2); break;
+                case 'M': freedup(erg->mgr_server, argv[s]+2); break;
+                case 'P': freedup(erg->pt_server, argv[s]+2); break;
+                case 'T': {
+                    const char *ipport = argv[s]+2;
+                    if (ipport[0] == ':' &&
+                        ipport[1] >= '0' && ipport[1] <= '9') { // port only -> assume localhost
+                        erg->tcp = GBS_global_string_copy("localhost%s", ipport);
+                    }
+                    else {
+                        erg->tcp = strdup(ipport);
+                    }
+                    break;
+                }
+                default:
+                    argv[d++] = argv[s];
+                    break;
+            }
+        }
+        else {
+            argv[d++] = argv[s];
+        }
+    }
+    *argc = d;
+    return erg;
+}
+
+void free_arb_params(arb_params *params) {
+    free(params->species_name);
+    free(params->extended_name);
+    free(params->alignment);
+    free(params->default_file);
+    free(params->field);
+    free(params->job_server);
+    free(params->db_server);
+    free(params->mgr_server);
+    free(params->pt_server);
+    free(params->tcp);
+
+    free(params);
+}
+
+// --------------------------------------------------------------------------------
+
+#if defined(UNIT_TESTS) 
+
+// If you need tests in AISC_COM/C/client.c, put them here instead.
+
+#include <test_unit.h>
+
+void TEST_servercntrl() {
+    // TEST_EXPECT(0);
+}
+
+#endif // UNIT_TESTS
+

SERVERCNTRL/servercntrl.h

+/* This file is generated by aisc_mkpt.
+ * Any changes you make here will be overwritten later!
+ */
+
+#ifndef SERVERCNTRL_H
+#define SERVERCNTRL_H
+
+
+/* servercntrl.cxx */
+
+#ifndef ARBDB_BASE_H
+#include <arbdb_base.h>
+#endif
+
+struct arb_params {
+    char *species_name;
+    char *extended_name;
+    char *alignment;
+    char *default_file;
+    char *field;
+    const char *field_default;
+
+    int  read_only;
+
+    char *job_server;
+    char *db_server;
+    char *mgr_server;
+    char *pt_server;
+
+    char *tcp;
+};
+
+char *prefixSSH(const char *host, const char *command, int async);
+GB_ERROR arb_start_server(const char *arb_tcp_env, int do_sleep);
+GB_ERROR arb_look_and_start_server(long magic_number, const char *arb_tcp_env);
+GB_ERROR arb_look_and_kill_server(int magic_number, const char *arb_tcp_env);
+void arb_print_server_params(void);
+arb_params *arb_trace_argv(int *argc, const char **argv);
+void free_arb_params(arb_params *params);
+
+#else
+#error servercntrl.h included twice
+#endif /* SERVERCNTRL_H */

SL/CB/cb.h

+// ================================================================= //
+//                                                                   //
+//   File      : cb.h                                                //
+//   Purpose   : callback                                            //
+//                                                                   //
+//   Coded by Ralf Westram (coder@reallysoft.de) in September 2010   //
+//   Institute of Microbiology (Technical University Munich)         //
+//   http://www.arb-home.de/                                         //
+//                                                                   //
+// ================================================================= //
+
+#ifndef CB_H
+#define CB_H
+
+#ifndef ARBDB_BASE_H
+#include <arbdb_base.h>
+#endif
+
+class AW_root;
+class AW_window;
+class AW_awar;
+
+// generic callback parameter (used like a void*)
+typedef long AW_CL; // client data (casted from pointer or value)
+
+// Note:
+// most callbacks below are considered obsolete (as soon as #432 is completed)
+// They are mostly used to cast functions; better use make....Callback-wrappers 
+
+// AW_root callbacks
+typedef void (*AW_RCB2)(AW_root*, AW_CL, AW_CL);
+typedef void (*AW_RCB1)(AW_root*, AW_CL);
+typedef void (*AW_RCB0)(AW_root*);
+typedef AW_RCB2 AW_RCB;
+
+// AW_awar callbacks
+typedef AW_RCB2 Awar_CB2;
+typedef AW_RCB1 Awar_CB1;
+typedef AW_RCB0 Awar_CB0;
+typedef AW_RCB  Awar_CB;
+
+// AW_window callbacks
+typedef void (*AW_CB2)(AW_window*, AW_CL, AW_CL);
+typedef void (*AW_CB1)(AW_window*, AW_CL);
+typedef void (*AW_CB0)(AW_window*);
+typedef AW_CB2 AW_CB;
+
+// simplest callback flavours of each type
+typedef AW_window *(*CreateWindowCallbackSimple)(AW_root*); // use makeCreateWindowCallback if you need parameters
+typedef AW_RCB0 RootCallbackSimple;                         // use makeRootCallback if you need parameters
+typedef AW_CB0  WindowCallbackSimple;                       // use makeWindowCallback if you need parameters
+
+// ---------------------------
+//      typesafe callbacks
+
+#ifndef CBTYPES_H
+#include <cbtypes.h>
+#endif
+
+// @@@ when gtk port is back to trunk, the definition of some of these cb-types may be moved into WINDOW
+
+DECLARE_CBTYPE_FVV_AND_BUILDERS(RootCallback,         void,       AW_root*);   // generates makeRootCallback
+DECLARE_CBTYPE_FVV_AND_BUILDERS(TimedCallback,        unsigned,   AW_root*);   // generates makeTimedCallback (return value: 0->do not call again, else: call again after XXX ms)
+DECLARE_CBTYPE_FVV_AND_BUILDERS(WindowCallback,       void,       AW_window*); // generates makeWindowCallback
+DECLARE_CBTYPE_FVV_AND_BUILDERS(CreateWindowCallback, AW_window*, AW_root*);   // generates makeCreateWindowCallback
+
+DECLARE_CBTYPE_FVF_AND_BUILDERS(DatabaseCallback, void, GBDATA*, GB_CB_TYPE);    // generates makeDatabaseCallback
+
+DECLARE_CBTYPE_FFV_AND_BUILDERS(TreeAwarCallback, void, AW_awar*, bool); // generates makeTreeAwarCallback
+
+#else
+#error cb.h included twice
+#endif // CB_H

SL/TRANSLATE/Translate.hxx → SL/CB/cb_base.h

-// =============================================================== //
-//                                                                 //
-//   File      : Translate.hxx                                     //
-//   Purpose   :                                                   //
-//                                                                 //
-//   Coded by Ralf Westram (coder@reallysoft.de) in June 2006      //
-//   Institute of Microbiology (Technical University Munich)       //
-//   http://www.arb-home.de/                                       //
-//                                                                 //
-// =============================================================== //
+// ================================================================ //
+//                                                                  //
+//   File      : cb_base.h                                          //
+//   Purpose   : base types for interfaces                          //
+//                                                                  //
+//   Coded by Ralf Westram (coder@reallysoft.de) in November 2013   //
+//   Institute of Microbiology (Technical University Munich)        //
+//   http://www.arb-home.de/                                        //
+//                                                                  //
+// ================================================================ //
 
-#ifndef TRANSLATE_HXX
-#define TRANSLATE_HXX
+#ifndef CB_BASE_H
+#define CB_BASE_H
 
-#ifndef ARBDB_BASE_H
-#include <arbdb_base.h>
-#endif
-
-
-GB_ERROR AWT_getTranslationInfo(GBDATA *gb_species, int& arb_transl_table, int &codon_start);
-GB_ERROR AWT_saveTranslationInfo(GBDATA *gb_species, int arb_transl_table, int codon_start);
-GB_ERROR AWT_removeTranslationInfo(GBDATA *gb_species);
-
-int AWT_pro_a_nucs_convert(int arb_code_nr, char *data, size_t size, size_t pos, bool translate_all, bool create_start_codon, bool append_stop_codon, int *translatedSize);
+typedef struct Unfixed_cb_parameter *UNFIXED; // Unfixed_cb_parameter does not exist (intentionally!)
 
 #else
-#error Translate.hxx included twice
-#endif // TRANSLATE_HXX
+#error cb_base.h included twice
+#endif // CB_BASE_H

SL/CB/cbtypes.h

+// ============================================================== //
+//                                                                //
+//   File      : cbtypes.h                                        //
+//   Purpose   : generic cb types                                 //
+//                                                                //
+//   Coded by Ralf Westram (coder@reallysoft.de) in August 2011   //
+//   Institute of Microbiology (Technical University Munich)      //
+//   http://www.arb-home.de/                                      //
+//                                                                //
+// ============================================================== //
+
+#ifndef CBTYPES_H
+#define CBTYPES_H
+
+#ifndef CB_BASE_H
+#include "cb_base.h"
+#endif
+#ifndef TTYPES_H
+#include <ttypes.h>
+#endif
+#ifndef STATIC_ASSERT_H
+#include <static_assert.h>
+#endif
+#ifndef SMARTPTR_H
+#include <smartptr.h>
+#endif
+
+
+// ---------------------------------
+//      function type inspection
+
+template<typename RT, typename P1, typename P2, typename P3>
+struct Function {
+    enum { NumParams = 3 };
+    typedef RT (*Type)(P1,P2,P3);
+    typedef RT ResultType;
+};
+template<typename RT, typename P1, typename P2>
+struct Function<RT, P1, P2, void> {
+    enum { NumParams = 2 };
+    typedef RT (*Type)(P1,P2);
+};
+template<typename RT, typename P1>
+struct Function<RT, P1, void, void> {
+    enum { NumParams = 1 };
+    typedef RT (*Type)(P1);
+};
+template<typename RT>
+struct Function<RT, void, void, void> {
+    enum { NumParams = 0 };
+    typedef RT (*Type)();
+};
+
+// ---------------------------
+//      forward parameters
+
+template<typename T>
+struct ForwardParamT {
+    typedef typename IfThenElseType< TypeT<T>::IsClassT,
+                                     typename TypeOp<T>::RefConstT,
+                                     typename TypeOp<T>::ArgT >::ResultType Type;
+};
+
+template<typename T>
+struct ForwardParamT<T*> {
+    typedef typename TypeOp<T>::ArgT *Type;
+};
+template<> class ForwardParamT<void> { class Unused {}; public: typedef Unused Type; };
+
+// ------------------------------
+//      const parameter types
+
+template<typename T>
+struct ConstParamT {
+    typedef typename IfThenElseType< TypeT<T>::IsClassT,
+                                     typename TypeOp<T>::RefConstT,
+                                     typename TypeOp<T>::ConstT >::ResultType Type;
+};
+template<typename T>
+struct ConstParamT<T*> {
+    typedef typename TypeOp<T>::ConstT *Type;
+};
+template<> class ConstParamT<void> { class Unused {}; public: typedef Unused Type; };
+
+// ------------------------------------
+//      forbid some parameter types
+
+template<typename T> class AW_CL_castableType { public: static AW_CL cast_to_AW_CL(const T& t) { return (AW_CL)t; } };
+
+#define INVALID_CB_PARAM_TYPE(TYPE) template<> class AW_CL_castableType<TYPE> { }
+
+INVALID_CB_PARAM_TYPE(void);
+INVALID_CB_PARAM_TYPE(double);
+INVALID_CB_PARAM_TYPE(float);
+
+#undef INVALID_CB_PARAM_TYPE
+
+// -----------------------
+//      typed callback
+
+template<typename RT, typename P1 = void, typename P2 = void, typename P3 = void>
+struct StrictlyTypedCallback {
+    typedef typename Function<RT,P1,P2,P3>::Type FuncType;
+
+private:
+    typedef typename ForwardParamT<P1>::Type FP1;
+    typedef typename ForwardParamT<P2>::Type FP2;
+    typedef typename ForwardParamT<P3>::Type FP3;
+
+    FuncType cb;
+
+public:
+    enum { NumParams = Function<RT,P1,P2,P3>::NumParams };
+
+    StrictlyTypedCallback(FuncType CB) : cb(CB) {}
+
+    RT operator()(FP1 p1, FP2 p2, FP3 p3) const { return cb(p1, p2, p3); }
+    RT operator()(FP1 p1, FP2 p2)         const { return cb(p1, p2); }
+    RT operator()(FP1 p1)                 const { return cb(p1); }
+    RT operator()()                       const { return cb(); }
+
+    bool equals(const StrictlyTypedCallback& other) const { return cb == other.cb; }
+
+    AW_CL get_cb() const { return (AW_CL)cb; }
+    static StrictlyTypedCallback make_cb(AW_CL cb_) { return StrictlyTypedCallback((FuncType)cb_); }
+
+    bool is_set() const { return cb != 0; }
+
+    bool operator <  (const StrictlyTypedCallback& other) const { return cb <  other.cb; }
+    bool operator == (const StrictlyTypedCallback& other) const { return cb == other.cb; }
+};
+
+// ---------------------
+//      CallbackData
+
+template<typename P1, typename P2>
+struct CallbackData {
+    P1 p1;
+    P2 p2;
+
+    typedef void (*CallbackDataDeallocator)(P1 p1, P2 p2);
+    CallbackDataDeallocator dealloc;
+
+    CallbackData(P1 p1_, P2 p2_) : p1(p1_), p2(p2_), dealloc(NULL) {}
+    CallbackData(P1 p1_, P2 p2_, CallbackDataDeallocator dealloc_) : p1(p1_), p2(p2_), dealloc(dealloc_) {}
+    ~CallbackData() { if (dealloc) dealloc(p1, p2); }
+    bool operator <  (const CallbackData& other) const {
+        return p1<other.p1 || (p1 == other.p1 && (p2< other.p2 || (p2 == other.p2 && dealloc<other.dealloc)));
+    }
+    bool operator == (const CallbackData& other) const {
+        return p1 == other.p1 && p2 == other.p2 && dealloc == other.dealloc;
+    }
+};
+
+typedef CallbackData<AW_CL,AW_CL> UntypedCallbackData;
+
+// ------------------------------
+//      casted callback types
+
+template<typename RT, typename FIXED>
+struct Callback_FVV { // FVV stands for arguments (FIXED, VARIABLE, VARIABLE)
+    typedef StrictlyTypedCallback<RT,FIXED,AW_CL,AW_CL> Signature;
+
+private:
+    Signature                     cb;
+    SmartPtr<UntypedCallbackData> cd;
+
+public:
+    Callback_FVV(Signature CB, AW_CL P1, AW_CL P2) : cb(CB), cd(new UntypedCallbackData(P1, P2)) {}
+    Callback_FVV(Signature CB, UntypedCallbackData::CallbackDataDeallocator dealloc, AW_CL P1, AW_CL P2) : cb(CB), cd(new UntypedCallbackData(P1, P2, dealloc)) {}
+
+    RT operator()(FIXED fixed) const { return cb(fixed, cd->p1, cd->p2); }
+
+    bool operator <  (const Callback_FVV& other) const { return cb<other.cb || (cb == other.cb && *cd<*other.cd); }
+    bool operator == (const Callback_FVV& other) const { return cb == other.cb && *cd == *other.cd; }
+
+    bool same_function_as(const Callback_FVV& other) const { return cb == other.cb; }
+
+    AW_CL callee() const { return cb.get_cb(); } // @@@ only intermediate - remove later
+    AW_CL inspect_CD1() const { return cd->p1; } // @@@ only intermediate - remove later
+    AW_CL inspect_CD2() const { return cd->p2; } // @@@ only intermediate - remove later
+};
+
+template<typename RT, typename F1, typename F2>
+struct Callback_FFV { // FFV stands for arguments (FIXED, FIXED, VARIABLE)
+    typedef StrictlyTypedCallback<RT,F1,F2,AW_CL> Signature;
+
+private:
+    typedef CallbackData<AW_CL, AW_CL> FFV_CallbackData; // 2nd AW_CL is unused
+
+    Signature                  cb;
+    SmartPtr<FFV_CallbackData> cd;
+
+public:
+    Callback_FFV(Signature CB, AW_CL P)
+        : cb(CB),
+          cd(new FFV_CallbackData(P, 0))
+    {}
+
+    RT operator()(F1 f1, F2 f2) const { return cb(f1, f2, cd->p1); }
+};
+
+template<typename RT, typename F1, typename F2>
+struct Callback_FVF { // FVF stands for arguments (FIXED, VARIABLE, FIXED)
+    typedef StrictlyTypedCallback<RT,F1,AW_CL,F2>  SigP1;
+    typedef StrictlyTypedCallback<RT,F1,F2,void>   SigP0F12;
+    typedef StrictlyTypedCallback<RT,F2,void,void> SigP0F2;
+
+private:
+    enum funtype { ST_P0F12, ST_P0F2, ST_P1 }; // Signature type
+    typedef CallbackData<AW_CL,funtype> FVF_CallbackData;
+
+    AW_CL                      cb;  // has one of the above Signatures
+    SmartPtr<FVF_CallbackData> cd;  // cd->p2 cannot be used by clients and is used to select Signature of 'cb'
+
+    funtype get_funtype() const { return cd->p2; }
+
+public:
+    Callback_FVF(SigP0F12 CB) : cb(CB.get_cb()), cd(new FVF_CallbackData(0, ST_P0F12)) {}
+    Callback_FVF(SigP0F2 CB) : cb(CB.get_cb()), cd(new FVF_CallbackData(0, ST_P0F2)) {}
+    Callback_FVF(SigP1 CB, AW_CL P1) : cb(CB.get_cb()), cd(new FVF_CallbackData(P1, ST_P1)) {}
+    Callback_FVF(SigP1 CB, UntypedCallbackData::CallbackDataDeallocator dealloc, AW_CL P1)
+        : cb(CB.get_cb()), cd(new FVF_CallbackData(P1, ST_P1, (typename FVF_CallbackData::CallbackDataDeallocator)dealloc)) {}
+
+    RT operator()(F1 f1, F2 f2) const {
+        funtype ft = get_funtype();
+        if (ft == ST_P0F12) return SigP0F12::make_cb(cb)(f1, f2);
+        if (ft == ST_P0F2) return SigP0F2::make_cb(cb)(f2);
+        arb_assert(ft == ST_P1);
+        return SigP1::make_cb(cb)(f1, cd->p1, f2);
+    }
+
+    bool operator <  (const Callback_FVF& other) const { return cb<other.cb || (cb == other.cb && *cd<*other.cd); }
+    bool operator == (const Callback_FVF& other) const { return cb == other.cb && *cd == *other.cd; }
+
+    bool same_function_as(const Callback_FVF& other) const { return cb == other.cb; }
+
+    AW_CL callee() const { return cb; }          // @@@ only intermediate - remove later
+    AW_CL inspect_CD1() const { return cd->p1; } // @@@ only intermediate - remove later
+    AW_CL inspect_CD2() const { return cd->p2; } // @@@ only intermediate - remove later
+};
+
+
+// ---------------------------
+//      convenience macros
+
+#define CASTABLE_TO_AW_CL(TYPE)   (sizeof(TYPE) <= sizeof(AW_CL))
+#define CAST_TO_AW_CL(TYPE,PARAM) AW_CL_castableType<TYPE>::cast_to_AW_CL(PARAM)
+
+#define CONST_PARAM_T(T) typename ConstParamT<T>::Type 
+
+#define CBTYPE_FVV_BUILDER_NP(BUILDER,CB,RESULT,FIXED,SIG)      \
+    inline CB BUILDER(RESULT (*cb)(FIXED)) {                    \
+        return CB((SIG)cb, 0, 0);                               \
+    }
+
+
+#define CBTYPE_FVV_BUILDER_P1(BUILDER,CB,RESULT,FIXED,SIG,P1,P1fun)                                             \
+    template<typename P1>                                                                                       \
+    inline CB BUILDER(RESULT (*cb)(FIXED, P1fun), P1 p1) {                                                      \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P1));                                                                   \
+        return CB((SIG)cb, CAST_TO_AW_CL(P1,p1), 0);                                                            \
+    }                                                                                                           \
+    template<typename P1>                                                                                       \
+    inline CB BUILDER(RESULT (*cb)(FIXED, P1fun),                                                               \
+                      void (*dealloc)(P1), P1 p1) {                                                             \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P1));                                                                   \
+        return CB((SIG)cb, (UntypedCallbackData::CallbackDataDeallocator)dealloc, CAST_TO_AW_CL(P1,p1), 0);     \
+    }
+
+#define CBTYPE_FVV_BUILDER_P1P2(BUILDER,CB,RESULT,FIXED,SIG,P1,P2,P1fun,P2fun) \
+    template<typename P1, typename P2>                                  \
+    inline CB BUILDER(RESULT (*cb)(FIXED, P1fun, P2fun),                \
+                      P1 p1, P2 p2) {                                   \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P1) && CASTABLE_TO_AW_CL(P2));  \
+        return CB((SIG)cb, CAST_TO_AW_CL(P1,p1), CAST_TO_AW_CL(P2,p2)); \
+    }                                                                   \
+    template<typename P1, typename P2>                                  \
+    inline CB BUILDER(RESULT (*cb)(FIXED, P1fun, P2fun),                \
+                      void (*dealloc)(P1,P2), P1 p1, P2 p2) {           \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P1) && CASTABLE_TO_AW_CL(P2));  \
+        return CB((SIG)cb, (UntypedCallbackData::CallbackDataDeallocator)dealloc, CAST_TO_AW_CL(P1,p1), CAST_TO_AW_CL(P2,p2)); \
+    }
+
+#define CBTYPE_FVV_BUILDER_NP12(BUILDER,CB,RESULT,FIXED,SIG,P1,P2)                                      \
+    CBTYPE_FVV_BUILDER_NP(BUILDER,CB,RESULT,FIXED,SIG);                                                 \
+    CBTYPE_FVV_BUILDER_P1(BUILDER,CB,RESULT,FIXED,SIG,P1,P1);                                           \
+    CBTYPE_FVV_BUILDER_P1(BUILDER,CB,RESULT,FIXED,SIG,P1,CONST_PARAM_T(P1));                            \
+    CBTYPE_FVV_BUILDER_P1P2(BUILDER,CB,RESULT,FIXED,SIG,P1,P2,P1,P2);                                   \
+    CBTYPE_FVV_BUILDER_P1P2(BUILDER,CB,RESULT,FIXED,SIG,P1,P2,P1,CONST_PARAM_T(P2));                    \
+    CBTYPE_FVV_BUILDER_P1P2(BUILDER,CB,RESULT,FIXED,SIG,P1,P2,CONST_PARAM_T(P1),P2);                    \
+    CBTYPE_FVV_BUILDER_P1P2(BUILDER,CB,RESULT,FIXED,SIG,P1,P2,CONST_PARAM_T(P1),CONST_PARAM_T(P2))
+
+#define CBTYPE_FVV_BUILDER_TEMPLATES(BUILDER,CB,RESULT,FIXED,SIG)                                       \
+    inline CB BUILDER(RESULT (*cb)()) {                                                                 \
+        return CB((SIG)cb, 0, 0);                                                                       \
+    }                                                                                                   \
+    CBTYPE_FVV_BUILDER_NP12(BUILDER,CB,RESULT,FIXED,SIG,P1,P2);                                         \
+    CBTYPE_FVV_BUILDER_NP12(BUILDER,CB,RESULT,UNFIXED,SIG,P1,P2)
+
+#define CBTYPE_FVV_BUILDER_P(BUILDER,CB,RESULT,F1,F2,SIG,P,Pfun)                                        \
+    template<typename P>                                                                                \
+    inline CB BUILDER(RESULT (*cb)(F1,F2,Pfun), P p) {                                                  \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P));                                                            \
+        return CB((SIG)cb, CAST_TO_AW_CL(P,p));                                                         \
+    }                                                                                                   \
+    template<typename P>                                                                                \
+    inline CB BUILDER(RESULT (*cb)(F1,F2,Pfun), void (*dealloc)(P), P p) {                              \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P));                                                            \
+        return CB((SIG)cb, (UntypedCallbackData::CallbackDataDeallocator)dealloc, CAST_TO_AW_CL(P,p));  \
+    }
+
+#define CBTYPE_FFV_BUILDER_TEMPLATES(BUILDER,CB,RESULT,F1,F2,SIG)          \
+    inline CB BUILDER(RESULT (*cb)()) { return CB((SIG)cb, 0); }           \
+    inline CB BUILDER(RESULT (*cb)(F1)) { return CB((SIG)cb, 0); }         \
+    inline CB BUILDER(RESULT (*cb)(F1,F2)) { return CB((SIG)cb, 0); }      \
+    CBTYPE_FVV_BUILDER_P(BUILDER,CB,RESULT,F1,F2,SIG,P,P);                 \
+    CBTYPE_FVV_BUILDER_P(BUILDER,CB,RESULT,F1,F2,SIG,P,CONST_PARAM_T(P))
+
+#define CBTYPE_FVF_BUILDER_P1_F1F2(BUILDER,CB,RESULT,F1,F2,SIG,P1,P1fun)                                        \
+    template<typename P1>                                                                                       \
+    inline CB BUILDER(RESULT (*cb)(F1, P1fun, F2), P1 p1) {                                                     \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P1));                                                                   \
+        return CB((SIG)cb, CAST_TO_AW_CL(P1,p1));                                                               \
+    }                                                                                                           \
+    template<typename P1>                                                                                       \
+    inline CB BUILDER(RESULT (*cb)(F1, P1fun, F2),                                                              \
+                      void (*dealloc)(P1), P1 p1) {                                                             \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P1));                                                                   \
+        return CB((SIG)cb, (UntypedCallbackData::CallbackDataDeallocator)dealloc, CAST_TO_AW_CL(P1,p1));        \
+    }
+
+#define CBTYPE_FVF_BUILDER_P1_F1(BUILDER,CB,RESULT,F1,SIG,P1,P1fun)                                             \
+    template<typename P1>                                                                                       \
+    inline CB BUILDER(RESULT (*cb)(F1, P1fun), P1 p1) {                                                         \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P1));                                                                   \
+        return CB((SIG)cb, CAST_TO_AW_CL(P1,p1));                                                               \
+    }                                                                                                           \
+    template<typename P1>                                                                                       \
+    inline CB BUILDER(RESULT (*cb)(F1, P1fun),                                                                  \
+                      void (*dealloc)(P1), P1 p1) {                                                             \
+        STATIC_ASSERT(CASTABLE_TO_AW_CL(P1));                                                                   \
+        return CB((SIG)cb, (UntypedCallbackData::CallbackDataDeallocator)dealloc, CAST_TO_AW_CL(P1,p1));        \
+    }
+
+#define CBTYPE_FVF_BUILDER_NP1(BUILDER,CB,RESULT,F1,F2,SIG,SIG01,P1)                    \
+    inline CB BUILDER(RESULT (*cb)(F1)) { return CB((SIG01)cb); }                       \
+    inline CB BUILDER(RESULT (*cb)(F1,F2)) { return CB((SIG01)cb); }                    \
+    CBTYPE_FVF_BUILDER_P1_F1F2(BUILDER,CB,RESULT,F1,F2,SIG,P1,P1);                      \
+    CBTYPE_FVF_BUILDER_P1_F1F2(BUILDER,CB,RESULT,F1,F2,SIG,P1,CONST_PARAM_T(P1));       \
+    CBTYPE_FVF_BUILDER_P1_F1(BUILDER,CB,RESULT,F1,SIG,P1,P1);                           \
+    CBTYPE_FVF_BUILDER_P1_F1(BUILDER,CB,RESULT,F1,SIG,P1,CONST_PARAM_T(P1))
+
+#define CBTYPE_FVF_BUILDER_TEMPLATES(BUILDER,CB,RESULT,F1,F2,SIG,SIG01,SIG02)           \
+    inline CB BUILDER(RESULT (*cb)()) { return CB((SIG01)cb); }                         \
+    inline CB BUILDER(RESULT (*cb)(F2)) { return CB((SIG02)cb); }                       \
+    CBTYPE_FVF_BUILDER_NP1(BUILDER,CB,RESULT,F1,F2,SIG,SIG01,P1);                       \
+    CBTYPE_FVF_BUILDER_NP1(BUILDER,CB,RESULT,UNFIXED,F2,SIG,SIG01,P1)
+
+// declares the callback type (CBTYPE) and the makeCBTYPE() templates needed to ensure
+// typecheck between callback-signature and bound parameters
+
+#define DECLARE_CBTYPE_FVV_AND_BUILDERS(CBTYPE,RESULT,FIXED)            \
+    typedef Callback_FVV<RESULT, FIXED> CBTYPE;                         \
+    CBTYPE_FVV_BUILDER_TEMPLATES(make##CBTYPE,CBTYPE,RESULT,FIXED,      \
+                                 CBTYPE::Signature::FuncType)
+
+#define DECLARE_CBTYPE_FFV_AND_BUILDERS(CBTYPE,RESULT,F1,F2)            \
+    typedef Callback_FFV<RESULT,F1,F2> CBTYPE;                          \
+    CBTYPE_FFV_BUILDER_TEMPLATES(make##CBTYPE,CBTYPE,RESULT,F1,F2,      \
+                                 CBTYPE::Signature::FuncType)
+
+#define DECLARE_CBTYPE_FVF_AND_BUILDERS(CBTYPE,RESULT,F1,F2)            \
+    typedef Callback_FVF<RESULT,F1,F2> CBTYPE;                          \
+    CBTYPE_FVF_BUILDER_TEMPLATES(make##CBTYPE,CBTYPE,RESULT,F1,F2,      \
+                                 CBTYPE::SigP1::FuncType,               \
+                                 CBTYPE::SigP0F12::FuncType,            \
+                                 CBTYPE::SigP0F2::FuncType)
+
+#else
+#error cbtypes.h included twice
+#endif // CBTYPES_H

SL/TRANSLATE/Makefile

-# for variables passed from parent makefile see ../../SOURCE_TOOLS/parent_make.txt
-
-.SUFFIXES: .o .c .cxx .depend
-
-C_OBJECTS = 
-CPP_OBJECTS = \
-	Translate.o \
-
-OBJECTS=$(C_OBJECTS) $(CPP_OBJECTS)
-
-$(MAIN): $(OBJECTS)
-	$(LINK_STATIC_LIB) $(MAIN) $(OBJECTS)
-
-.cxx.o:
-	$(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
-
-.c.o:
-	$(A_CC) $(cflags) -c $< $(CC_INCLUDES) $(POST_COMPILE)
-
-clean:
-	rm -f $(OBJECTS) *.a
-
-DEPENDS = $(OBJECTS:.o=.depend)
-depends: $(DEPENDS)
-	@cat $(DEPENDS) | grep -v '^#' >>Makefile
-	@rm $(DEPENDS)
-$(DEPENDS): depend.init
-depend.init:
-	$(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
-.c.depend:
-	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
-.cxx.depend:
-	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
-
-# DO NOT DELETE
-
-# Do not add dependencies manually - use 'make depend' in $ARBHOME
-# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from SL)
-
-Translate.o: Translate.hxx
-Translate.o: $(ARBHOME)/INCLUDE/ad_prot.h
-Translate.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-Translate.o: $(ARBHOME)/INCLUDE/AP_codon_table.hxx
-Translate.o: $(ARBHOME)/INCLUDE/AP_pro_a_nucs.hxx
-Translate.o: $(ARBHOME)/INCLUDE/arb_assert.h
-Translate.o: $(ARBHOME)/INCLUDE/arb_core.h
-Translate.o: $(ARBHOME)/INCLUDE/arb_error.h
-Translate.o: $(ARBHOME)/INCLUDE/arb_msg.h
-Translate.o: $(ARBHOME)/INCLUDE/arb_string.h
-Translate.o: $(ARBHOME)/INCLUDE/arbdb.h
-Translate.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-Translate.o: $(ARBHOME)/INCLUDE/arbdbt.h
-Translate.o: $(ARBHOME)/INCLUDE/arbtools.h
-Translate.o: $(ARBHOME)/INCLUDE/attributes.h
-Translate.o: $(ARBHOME)/INCLUDE/cxxforward.h
-Translate.o: $(ARBHOME)/INCLUDE/downcast.h
-Translate.o: $(ARBHOME)/INCLUDE/dupstr.h
-Translate.o: $(ARBHOME)/INCLUDE/gccver.h
-Translate.o: $(ARBHOME)/INCLUDE/smartptr.h
-Translate.o: $(ARBHOME)/INCLUDE/static_assert.h
-Translate.o: $(ARBHOME)/INCLUDE/test_global.h

SL/TRANSLATE/Translate.cxx

-// =============================================================== //
-//                                                                 //
-//   File      : AWT_translate.cxx                                 //
-//   Purpose   :                                                   //
-//                                                                 //
-//   Coded by Ralf Westram (coder@reallysoft.de) in June 2006      //
-//   Institute of Microbiology (Technical University Munich)       //
-//   http://www.arb-home.de/                                       //
-//                                                                 //
-// =============================================================== //
-
-#include "Translate.hxx"
-
-#include <AP_pro_a_nucs.hxx>
-#include <AP_codon_table.hxx>
-#include <arbdbt.h>
-
-#define tl_assert(cond) arb_assert(cond)
-
-GB_ERROR AWT_saveTranslationInfo(GBDATA *gb_species, int arb_transl_table, int codon_start) {
-    int embl_transl_table = AWT_arb_code_nr_2_embl_transl_table(arb_transl_table);
-
-    tl_assert(codon_start >= 0 && codon_start<3); // codon_start has to be 0..2
-    tl_assert(embl_transl_table >= 0);
-
-    GB_ERROR error    = GBT_write_string(gb_species, "transl_table", GBS_global_string("%i", embl_transl_table));
-    if (!error) error = GBT_write_string(gb_species, "codon_start",  GBS_global_string("%i", codon_start+1));
-
-    return error;
-}
-
-GB_ERROR AWT_removeTranslationInfo(GBDATA *gb_species) {
-    GB_ERROR error = NULL;
-
-    GBDATA *gb_transl_table    = GB_entry(gb_species, "transl_table");
-    if (gb_transl_table) error = GB_delete(gb_transl_table);
-
-    if (!error) {
-        GBDATA *gb_codon_start    = GB_entry(gb_species, "codon_start");
-        if (gb_codon_start) error = GB_delete(gb_codon_start);
-    }
-
-    return error;
-}
-
-GB_ERROR AWT_getTranslationInfo(GBDATA *gb_item, int& arb_transl_table, int& codon_start) {
-    // looks for sub-entries 'transl_table' and 'codon_start' of species (works for genes as well)
-    // if found -> test for validity and translate 'transl_table' from EMBL to ARB table number
-    //
-    // returns: an error in case of problems
-    //
-    // 'arb_transl_table' is set to -1 if not found, otherwise it contains the arb table number
-    // 'codon_start'      is set to -1 if not found, otherwise it contains the codon_start (0..2)
-
-    arb_transl_table = -1;          // not found yet
-    codon_start      = -1;          // not found yet
-
-    GB_ERROR  error           = 0;
-    GBDATA   *gb_transl_table = GB_entry(gb_item, "transl_table");
-
-    if (gb_transl_table) {
-        int embl_table   = atoi(GB_read_char_pntr(gb_transl_table));
-        arb_transl_table = AWT_embl_transl_table_2_arb_code_nr(embl_table);
-        if (arb_transl_table == -1) { // ill. table
-            error = GBS_global_string("Illegal (or unsupported) value (%i) in 'transl_table'", embl_table);
-        }
-    }
-
-    if (!error) {
-        GBDATA *gb_codon_start = GB_entry(gb_item, "codon_start");
-        if (gb_codon_start) {
-            int codon_start_value = atoi(GB_read_char_pntr(gb_codon_start));
-
-            if (codon_start_value<1 || codon_start_value>3) {
-                error = GBS_global_string("Illegal value (%i) in 'codon_start' (allowed: 1..3)", codon_start_value);
-            }
-            else {
-                codon_start = codon_start_value-1; // internal value is 0..2
-            }
-        }
-        else if (arb_transl_table != -1) {
-            // default to codon_start 1
-            error = GBT_write_string(gb_item, "codon_start", "1");
-            if (!error) codon_start = 0; // internal value is 0..2
-        }
-    }
-
-    if (!error && arb_transl_table != codon_start) {
-        if (arb_transl_table == -1) error = "Found 'codon_start', but 'transl_table' is missing";
-        else if (codon_start == -1) error = "Found 'transl_table', but 'codon_start' is missing";
-    }
-
-    if (error) { // append species name to error message
-        error = GBS_global_string("%s (item='%s')", error, GBT_read_name(gb_item));
-    }
-
-    return error;
-}
-
-inline void memcpy3(char *dest, const char *source) {
-    dest[0] = source[0];
-    dest[1] = source[1];
-    dest[2] = source[2];
-}
-
-int AWT_pro_a_nucs_convert(int arb_code_nr, char *data, size_t size, size_t pos, bool translate_all, bool create_start_codon, bool append_stop_codon, int *translatedSize) {
-    // if translate_all == true -> 'pos' > 1 produces a leading 'X' in protein data
-    //                             (otherwise nucleotides in front of the starting pos are simply ignored)
-    //
-    // if 'create_start_codon' is true and the first generated codon is a start codon of the used
-    //                                 code, a 'M' is inserted instead of the codon
-    // if 'append_stop_codon' is true, the stop codon is appended as '*'. This is only done, if the last
-    //                                 character not already is a stop codon. (Note: provide data with correct size)
-    //
-    // returns:
-    // - the translated protein sequence in 'data'
-    // - the length of the translated protein sequence in 'translatedSize' (if != 0)
-    // - number of stop-codons in translated sequence as result
-
-    arb_assert(pos <= 2);
-
-    for (char *p = data; *p;  p++) {
-        char c = *p;
-        if ((c>='a') && (c<='z')) c = c+'A'-'a';
-        if (c=='U') c = 'T';
-        *p = c;
-    }
-
-    char buffer[4];
-    buffer[3] = 0;
-
-    char *dest  = data;
-
-    if (pos && translate_all) {
-        for (char *p = data; p<data+pos; ++p) {
-            char c = *p;
-            if (c!='.' && c!='-') { // found a nucleotide
-                *dest++ = 'X';
-                break;
-            }
-        }
-    }
-
-    int            stops      = 0;
-    size_t         i          = pos;
-    char           startCodon = 0;
-    const GB_HASH *t2i_hash   = AWT_get_translator(arb_code_nr)->T2iHash();
-
-    if (create_start_codon) {
-        memcpy3(buffer, data+pos);
-        startCodon = AWT_is_start_codon(buffer, arb_code_nr);
-    }
-
-    for (char *p = data+pos; i+2<size; p+=3, i+=3) {
-        memcpy3(buffer, p);
-        int spro = (int)GBS_read_hash(t2i_hash, buffer);
-        int C;
-        if (!spro) {
-            C = 'X';
-        }
-        else {
-            if (spro == '*') stops++;
-            C = spro;
-            if (spro == 's') C = 'S';
-        }
-        *(dest++) = (char)C;
-    }
-
-    int tsize = dest-data;
-
-    if (tsize>0) {            // at least 1 amino written
-        if (create_start_codon && startCodon) data[0] = startCodon;
-        if (append_stop_codon && dest[-1] != '*') {
-            *dest++ = '*';
-            tsize++;
-        }
-    }
-    dest[0] = 0;
-
-    if (translatedSize) *translatedSize = tsize;
-
-    return stops;
-}
-
-
-
-
-

SL/TRANSLATE/needs_libs

-# libraries needed to link against SL/TRANSLATE/TRANSLATE.a
-
-SL/PRONUC/PRONUC.a
-

SL/TREEDISP/Makefile

-# for variables passed from parent makefile see ../../SOURCE_TOOLS/parent_make.txt
-
-.SUFFIXES: .o .c .cxx .hxx .depend
-
-C_OBJECTS = 
-CPP_OBJECTS = \
-	TreeDisplay.o \
-	irstree_display.o \
-	TreeCallbacks.o \
-
-OBJECTS=$(C_OBJECTS) $(CPP_OBJECTS)
-
-$(MAIN): $(OBJECTS)
-	$(LINK_STATIC_LIB) $(MAIN) $(OBJECTS)
-
-.cxx.o:
-	$(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
-
-.c.o:
-	$(A_CC) $(cflags) -c $< $(CC_INCLUDES) $(POST_COMPILE)
-
-proto:
-	../../AISC_MKPTPS/aisc_mkpt -P -w TreeCallbacks.hxx TreeCallbacks.cxx >TreeCallbacks.hxx.tmp
-	../../SOURCE_TOOLS/mv_if_diff TreeCallbacks.hxx.tmp TreeCallbacks.hxx
-
-clean:
-	rm -f $(OBJECTS) *.a
-
-DEPENDS = $(OBJECTS:.o=.depend)
-depends: $(DEPENDS)
-	@cat $(DEPENDS) | grep -v '^#' >>Makefile
-	@rm $(DEPENDS)
-$(DEPENDS): depend.init
-depend.init:
-	$(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
-.c.depend:
-	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
-.cxx.depend:
-	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
-
-# DO NOT DELETE
-
-# Do not add dependencies manually - use 'make depend' in $ARBHOME
-# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from SL)
-
-irstree_display.o: TreeDisplay.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/ad_prot.h
-irstree_display.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-irstree_display.o: $(ARBHOME)/INCLUDE/AliView.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/arb_assert.h
-irstree_display.o: $(ARBHOME)/INCLUDE/arb_core.h
-irstree_display.o: $(ARBHOME)/INCLUDE/arb_error.h
-irstree_display.o: $(ARBHOME)/INCLUDE/arb_msg.h
-irstree_display.o: $(ARBHOME)/INCLUDE/arb_string.h
-irstree_display.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/arbdb.h
-irstree_display.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-irstree_display.o: $(ARBHOME)/INCLUDE/arbdbt.h
-irstree_display.o: $(ARBHOME)/INCLUDE/arbtools.h
-irstree_display.o: $(ARBHOME)/INCLUDE/attributes.h
-irstree_display.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/aw_device.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/aw_device_click.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/aw_position.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
-irstree_display.o: $(ARBHOME)/INCLUDE/cb.h
-irstree_display.o: $(ARBHOME)/INCLUDE/cb_base.h
-irstree_display.o: $(ARBHOME)/INCLUDE/cbtypes.h
-irstree_display.o: $(ARBHOME)/INCLUDE/cxxforward.h
-irstree_display.o: $(ARBHOME)/INCLUDE/downcast.h
-irstree_display.o: $(ARBHOME)/INCLUDE/dupstr.h
-irstree_display.o: $(ARBHOME)/INCLUDE/gccver.h
-irstree_display.o: $(ARBHOME)/INCLUDE/nds.h
-irstree_display.o: $(ARBHOME)/INCLUDE/RootedTree.h
-irstree_display.o: $(ARBHOME)/INCLUDE/smartptr.h
-irstree_display.o: $(ARBHOME)/INCLUDE/static_assert.h
-irstree_display.o: $(ARBHOME)/INCLUDE/test_global.h
-irstree_display.o: $(ARBHOME)/INCLUDE/ttypes.h
-
-TreeCallbacks.o: TreeCallbacks.hxx
-TreeCallbacks.o: TreeDisplay.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/ad_prot.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/AliView.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arb_assert.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arb_core.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arb_error.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arb_msg.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arb_string.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arbdb.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arbdbt.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/arbtools.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/attributes.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_advice.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_awar_defs.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_device.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_device_click.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_position.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/cb.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/cb_base.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/cbtypes.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/cxxforward.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/downcast.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/dupstr.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/gccver.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/mode_text.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/RootedTree.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/smartptr.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/static_assert.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/test_global.h
-TreeCallbacks.o: $(ARBHOME)/INCLUDE/ttypes.h
-
-TreeDisplay.o: ../../WINDOW/aw_common.hxx
-TreeDisplay.o: TreeDisplay.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/ad_prot.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/AliView.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/AP_sequence.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/AP_Tree.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_assert.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_core.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_defs.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_diff.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_error.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_global_defs.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_msg.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_strarray.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arb_string.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/ARB_Tree.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arbdb.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arbdbt.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/arbtools.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/attributes.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_awar_defs.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_awars.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_color_groups.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_device.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_device_click.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_position.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_preset.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_question.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/awt_attributes.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/awt_canvas.hxx
-TreeDisplay.o: $(ARBHOME)/INCLUDE/cb.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/cb_base.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/cbtypes.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/cxxforward.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/downcast.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/dupstr.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/gccver.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/nds.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/RootedTree.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/smartptr.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/static_assert.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/test_global.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/test_unit.h
-TreeDisplay.o: $(ARBHOME)/INCLUDE/ttypes.h

SL/TREEDISP/TreeCallbacks.hxx

-/* This file is generated by aisc_mkpt.
- * Any changes you make here will be overwritten later!
- */
-
-#ifndef TREECALLBACKS_HXX
-#define TREECALLBACKS_HXX
-
-
-/* TreeCallbacks.cxx */
-
-#ifndef TREEDISPLAY_HXX
-#include <TreeDisplay.hxx>
-#endif
-
-void nt_mode_event(UNFIXED, AWT_canvas *ntw, AWT_COMMAND_MODE mode);
-void NT_mark_all_cb(UNFIXED, AWT_canvas *ntw, int mark_mode);
-void NT_insert_mark_submenus(AW_window_menu_modes *awm, AWT_canvas *ntw, int insert_as_submenu);
-void NT_group_tree_cb(UNFIXED, AWT_canvas *ntw);
-void NT_group_not_marked_cb(UNFIXED, AWT_canvas *ntw);
-void NT_group_terminal_cb(UNFIXED, AWT_canvas *ntw);
-void NT_ungroup_all_cb(UNFIXED, AWT_canvas *ntw);
-void NT_insert_color_collapse_submenu(AW_window_menu_modes *awm, AWT_canvas *ntree_canvas);
-GB_ERROR NT_with_displayed_tree_do(AWT_canvas *ntw, bool (*displayed_tree_cb)(RootedTree *tree, GB_ERROR& error));
-void NT_resort_tree_cb(UNFIXED, AWT_canvas *ntw, TreeOrder order);
-void NT_reset_lzoom_cb(UNFIXED, AWT_canvas *ntw);
-void NT_reset_pzoom_cb(UNFIXED, AWT_canvas *ntw);
-void NT_set_tree_style(UNFIXED, AWT_canvas *ntw, AP_tree_display_type type);
-void NT_remove_leafs(UNFIXED, AWT_canvas *ntw, AWT_RemoveType mode);
-void NT_remove_bootstrap(UNFIXED, AWT_canvas *ntw);
-void NT_toggle_bootstrap100(UNFIXED, AWT_canvas *ntw);
-void NT_reset_branchlengths(UNFIXED, AWT_canvas *ntw);
-void NT_multifurcate_tree(AWT_canvas *ntw, const RootedTree ::multifurc_limits& below);
-void NT_move_boot_branch(UNFIXED, AWT_canvas *ntw, int direction);
-void NT_scale_tree(UNFIXED, AWT_canvas *ntw);
-void NT_jump_cb(UNFIXED, AWT_canvas *ntw, AP_tree_jump_type jumpType);
-void TREE_auto_jump_cb(UNFIXED, AWT_canvas *ntw);
-void NT_reload_tree_event(AW_root *awr, AWT_canvas *ntw, bool expose);
-void TREE_recompute_cb(UNFIXED, AWT_canvas *ntw);
-void NT_reinit_treetype(UNFIXED, AWT_canvas *ntw);
-void NT_remove_species_in_tree_from_hash(AP_tree *tree, GB_HASH *hash);
-
-#else
-#error TreeCallbacks.hxx included twice
-#endif /* TREECALLBACKS_HXX */

SL/TREEDISP/TreeDisplay.hxx

-// =============================================================== //
-//                                                                 //
-//   File      : TreeDisplay.hxx                                   //
-//   Purpose   :                                                   //
-//                                                                 //
-//   Institute of Microbiology (Technical University Munich)       //
-//   http://www.arb-home.de/                                       //
-//                                                                 //
-// =============================================================== //
-
-#ifndef TREEDISPLAY_HXX
-#define TREEDISPLAY_HXX
-
-#ifndef AP_TREE_HXX
-#include <AP_Tree.hxx>
-#endif
-#ifndef AWT_CANVAS_HXX
-#include <awt_canvas.hxx>
-#endif
-
-#define td_assert(cond) arb_assert(cond)
-
-#define AWAR_DTREE_BASELINEWIDTH   "awt/dtree/baselinewidth"
-#define AWAR_DTREE_VERICAL_DIST    "awt/dtree/verticaldist"
-#define AWAR_DTREE_AUTO_JUMP       "awt/dtree/autojump"
-#define AWAR_DTREE_SHOW_CIRCLE     "awt/dtree/show_circle"
-#define AWAR_DTREE_SHOW_BRACKETS   "awt/dtree/show_brackets"
-#define AWAR_DTREE_CIRCLE_ZOOM     "awt/dtree/circle_zoom"
-#define AWAR_DTREE_CIRCLE_MAX_SIZE "awt/dtree/max_size"
-#define AWAR_DTREE_USE_ELLIPSE     "awt/dtree/ellipse"
-#define AWAR_DTREE_GREY_LEVEL      "awt/dtree/greylevel"
-
-#define AWAR_DTREE_RADIAL_ZOOM_TEXT "awt/dtree/radial/zoomtext"
-#define AWAR_DTREE_RADIAL_XPAD      "awt/dtree/radial/xpadding"
-
-#define AWAR_DTREE_DENDRO_ZOOM_TEXT "awt/dtree/dendro/zoomtext"
-#define AWAR_DTREE_DENDRO_XPAD      "awt/dtree/dendro/xpadding"
-
-void awt_create_dtree_awars(AW_root *aw_root, AW_default db);
-
-#define NT_BOX_WIDTH      7 // pixel
-#define NT_ROOT_WIDTH     9
-#define NT_SELECTED_WIDTH 11
-
-#define AWT_TREE(ntw) DOWNCAST(AWT_graphic_tree*, (ntw)->gfx)
-
-
-enum AP_tree_display_type {
-    AP_TREE_NORMAL, // normal tree display (dendrogram)
-    AP_TREE_RADIAL, // radial tree display
-    AP_TREE_IRS, // like AP_TREE_NORMAL, with folding line
-    AP_LIST_NDS,
-    AP_LIST_SIMPLE // simple display only showing name (used at startup to avoid NDS error messages)
-};
-
-enum AP_tree_jump_type { // bit-values
-    AP_JUMP_UNFOLD_GROUPS     = 1,
-    AP_JUMP_CENTER_IF_VISIBLE = 2, // if already visible -> center (normally only done if IRS-mode or selected was invisible)
-    AP_JUMP_BE_VERBOOSE       = 4, // tell why nothing happened etc.
-
-    // convenience defs:
-    AP_JUMP_AUTO      = 0,
-    AP_JUMP_BY_BUTTON = AP_JUMP_UNFOLD_GROUPS|AP_JUMP_CENTER_IF_VISIBLE|AP_JUMP_BE_VERBOOSE,
-};
-
-inline bool sort_is_list_style(AP_tree_display_type sort) { return sort == AP_LIST_NDS || sort == AP_LIST_SIMPLE; }
-inline bool sort_is_tree_style(AP_tree_display_type sort) { return !sort_is_list_style(sort); }
-
-
-class AWT_graphic_tree_group_state;
-
-struct AWT_scaled_font_limits {
-    double ascent;
-    double descent;
-    double height;
-    double width;
-
-    void init(const AW_font_limits& font_limits, double factor) {
-        ascent  = font_limits.ascent*factor;
-        descent = font_limits.descent*factor;
-        height  = font_limits.height*factor;
-        width   = font_limits.width*factor;
-    }
-};
-
-enum AD_MAP_VIEWER_TYPE {
-    ADMVT_NONE = 0,
-    ADMVT_INFO,
-    ADMVT_WWW,
-    ADMVT_SELECT
-};
-
-typedef void (*AD_map_viewer_cb)(GBDATA *gbd, AD_MAP_VIEWER_TYPE type);
-
-struct DendroSubtreeLimits {
-    double y_branch;                                // ypos of branch to subtree
-    double y_top;                                   // top ypos of whole subtree
-    double y_bot;                                   // bottom ypos of whole subtree
-    double x_right;                                 // rightmost xpos of whole subtree
-
-    void combine(const DendroSubtreeLimits& other) {
-        y_top   = std::min(y_top, other.y_top);
-        y_bot   = std::max(y_bot, other.y_bot);
-        x_right = std::max(x_right, other.x_right);
-    }
-};
-
-struct AWT_command_data {
-    /*! any kind of data which has to be stored between different events (e.g. to support drag&drop)
-     * Purpose of this class is to allow to delete such data w/o knowing anything else.
-     */
-    virtual ~AWT_command_data() {}
-};
-
-enum CollapseMode {
-    COLLAPSE_ALL      = 0,
-    EXPAND_MARKED     = 1, // do not collapse groups containing marked species
-    COLLAPSE_TERMINAL = 2, // do not collapse groups with subgroups
-    EXPAND_ALL        = 4,
-    EXPAND_COLOR      = 8, // do not collapse groups containing species with color == parameter 'color_group'
-};
-
-class AWT_graphic_tree : public AWT_graphic, virtual Noncopyable {
-    char         *species_name;
-    AW::Position  cursor;
-
-    int    baselinewidth;
-    int    show_brackets;
-    int    show_circle;
-    int    use_ellipse;
-    float  circle_zoom_factor;
-    float  circle_max_size;
-
-    int zombies; // # of zombies during last load()
-    int duplicates; // # of duplicates during last load()
-
-    AW_pos paint_irs_sub_tree(AP_tree *node, AW_pos x_offset); // returns y pos
-
-    void unload();
-
-    // variables - tree compatibility
-
-    AP_tree * tree_proto;
-    bool link_to_database; // link on load ?
-
-    double list_tree_ruler_y;
-    double irs_tree_ruler_scale_factor;
-
-    AWT_scaled_font_limits scaled_font;
-    double                 scaled_branch_distance; // vertical distance between branches (may be extra-scaled in options)
-
-    AW_pos grey_level;
-
-    AW_device *disp_device; // device for recursive functions
-
-    const AW_bitset line_filter, vert_line_filter, mark_filter, group_bracket_filter, bs_circle_filter;
-    const AW_bitset leaf_text_filter, group_text_filter, remark_text_filter, other_text_filter;
-    const AW_bitset ruler_filter, root_filter;
-
-    bool nds_show_all;
-
-    AD_map_viewer_cb  map_viewer_cb;
-    AWT_command_data  *cmd_data;
-
-    void scale_text_koordinaten(AW_device *device, int gc, double& x, double& y, double orientation, int flag);
-
-    // functions to compute displayinformation
-
-    void show_dendrogram(AP_tree *at, AW::Position& pen, DendroSubtreeLimits& limits);
-
-    void show_radial_tree(AP_tree *at,
-                          double   x_center,
-                          double   y_center,
-                          double   tree_sprad,
-                          double   tree_orientation,
-                          double   x_root,
-                          double   y_root);
-
-    void show_nds_list(GBDATA * gb_main, bool use_nds);
-    void show_irs_tree(AP_tree *at, double height);
-
-    void box(int gc, const AW::Position& pos, int pixel_width, bool filled);
-    void filled_box(int gc, const AW::Position& pos, int pixel_width) { box(gc, pos, pixel_width, true); }
-    void empty_box(int gc, const AW::Position& pos, int pixel_width) { box(gc, pos, pixel_width, false); }
-    void diamond(int gc, const AW::Position& pos, int pixel_width);
-
-    const char *ruler_awar(const char *name);
-
-    void set_line_attributes_for(AP_tree *at) const {
-        disp_device->set_line_attributes(at->gr.gc, at->get_linewidth()+baselinewidth, AW_SOLID);
-    }
-
-    virtual void read_tree_settings();
-    void update_structure() {
-        AP_tree *root = get_root_node();
-        if (root) root->compute_tree();
-    }
-    void apply_zoom_settings_for_treetype(AWT_canvas *ntw);
-
-    int draw_branch_line(int gc, const AW::Position& root, const AW::Position& leaf, AW_bitset filter) {
-        const AW_click_cd *old = disp_device->get_click_cd();
-        td_assert(old && old->get_cd1() && !old->get_cd2()); // cd1 should be the node
-
-        AW_click_cd branch(disp_device, old->get_cd1(), (AW_CL)"branch");
-        return disp_device->line(gc, root, leaf, filter);
-    }
-
-    bool warn_inappropriate_mode(AWT_COMMAND_MODE mode);
-
-protected:
-    void store_command_data(AWT_command_data *new_cmd_data) {
-        delete cmd_data;
-        cmd_data = new_cmd_data;
-    }
-    AWT_command_data *get_command_data() { return cmd_data; }
-
-public:
-
-    // *********** read only variables !!!
-
-    AW_root      *aw_root;
-    AP_tree_display_type  tree_sort;
-    AP_tree      *displayed_root; // root node of shown (sub-)tree; differs from real root if tree is zoomed logically
-    AP_tree_root *tree_static;
-    GBDATA       *gb_main;
-
-    // *********** public section
-
-    AWT_graphic_tree(AW_root *aw_root, GBDATA *gb_main, AD_map_viewer_cb map_viewer_cb);
-    ~AWT_graphic_tree() OVERRIDE;
-
-    AP_tree *get_root_node() { return tree_static ? tree_static->get_root_node() : NULL; }
-    bool is_logically_zoomed() { return displayed_root != get_root_node(); }
-
-    void init(RootedTreeNodeFactory *nodeMaker_, AliView *aliview, AP_sequence *seq_prototype, bool link_to_database_, bool insert_delete_cbs);
-    AW_gc_manager init_devices(AW_window *, AW_device *, AWT_canvas *ntw) OVERRIDE;
-
-    void show(AW_device *device) OVERRIDE;
-    const AW::Position& get_cursor() const { return cursor; }
-
-    void info(AW_device *device, AW_pos x, AW_pos y, AW_clicked_line *cl, AW_clicked_text *ct) OVERRIDE;
-
-private:
-    void handle_key(AW_device *device, AWT_graphic_event& event);
-public:
-    void handle_command(AW_device *device, AWT_graphic_event& event) OVERRIDE;
-
-    void mark_species_in_tree(AP_tree *at, int mark);
-    void mark_species_in_tree_that(AP_tree *at, int mark, int (*condition)(GBDATA*, void*), void *cd);
-
-    void mark_species_in_rest_of_tree(AP_tree *at, int mark);
-    void mark_species_in_rest_of_tree_that(AP_tree *at, int mark, int (*condition)(GBDATA*, void*), void *cd);
-
-    bool tree_has_marks(AP_tree *at);
-    bool rest_tree_has_marks(AP_tree *at);
-
-    void detect_group_state(AP_tree *at, AWT_graphic_tree_group_state *state, AP_tree *skip_this_son);
-
-    bool     group_tree(AP_tree *at, CollapseMode mode, int color_group);
-    void     group_rest_tree(AP_tree *at, CollapseMode mode, int color_group);
-    void     reorder_tree(TreeOrder mode);
-    GB_ERROR create_group(AP_tree * at) __ATTR__USERESULT;
-    void     toggle_group(AP_tree * at);
-    GB_ERROR load(GBDATA *gb_main, const char *name, AW_CL,  AW_CL) OVERRIDE __ATTR__USERESULT;
-    GB_ERROR save(GBDATA *gb_main, const char *name, AW_CL cd1, AW_CL cd2) OVERRIDE __ATTR__USERESULT;
-    int      check_update(GBDATA *gb_main) OVERRIDE;         // reload tree if needed
-    void     update(GBDATA *gb_main) OVERRIDE;
-    void     set_tree_type(AP_tree_display_type type, AWT_canvas *ntw);
-
-    double get_irs_tree_ruler_scale_factor() const { return irs_tree_ruler_scale_factor; }
-    void show_ruler(AW_device *device, int gc);
-    void get_zombies_and_duplicates(int& zomb, int& dups) const { zomb = zombies; dups = duplicates; }
-
-#if defined(UNIT_TESTS) // UT_DIFF
-    friend class fake_AWT_graphic_tree;
-#endif
-};
-
-class ClickedTarget {
-    /*! Represents any target corresponding to some (mouse-)position in the tree display.
-     *
-     * The target is e.g. used as target for keystrokes or mouse clicks.
-     *
-     * For AP_LIST_NDS, this only represents the species (w/o any tree information).
-     * For other tree display modes, this represents a specific tree node.
-     *
-     * The space outside the tree does represent the whole tree (aka the root-node).
-     * (the necessary distance to the tree-structure/-text is defined by AWT_CATCH)
-     */
-
-    AP_tree *tree_node;
-    GBDATA  *gb_species;
-    bool     ruler;
-    bool     branch;
-
-    const AW_clicked_element *elem;
-
-    void init() {
-        tree_node  = NULL;
-        gb_species = NULL;
-        ruler      = false;
-        branch     = false;
-    }
-
-    void identify(AWT_graphic_tree *agt) {
-        init();
-        if (elem && elem->exists) {
-            const char *what = (const char*)elem->cd2();
-
-            if (what) {
-                if (strcmp(what, "species") == 0) { // entry in NDS list
-                    gb_species = (GBDATA*)elem->cd1();
-                    td_assert(gb_species);
-                }
-                else if (strcmp(what, "ruler") == 0) {
-                    ruler = !elem->cd1();
-                }
-                else if (strcmp(what, "branch") == 0) {
-                    branch = true; // indicates that a line really IS the branch (opposed to other branch-related lines like e.g. group-brackets)
-                }
-                else {
-                    td_assert(0); // unknown element type
-                }
-            }
-
-            if (!(gb_species || ruler)) {
-                tree_node = (AP_tree*)elem->cd1();
-                td_assert(branch || !what);
-            }
-        }
-        else { // use whole tree if mouse does not point to a subtree
-            tree_node = agt ? agt->get_root_node() : NULL;
-        }
-        td_assert(implicated(branch, tree_node));
-    }
-
-public:
-
-    ClickedTarget(AWT_graphic_tree *agt, const AW_clicked_element *clicked) : elem(clicked) {
-        // uses root of tree as target, when a position outside of the tree is selected
-        // (e.g. used for key-commands)
-        identify(agt);
-    }
-    ClickedTarget(const AW_clicked_element *clicked) : elem(clicked) {
-        // accept only normal branches as targets
-        identify(NULL);
-    }
-
-    const AW_clicked_element *element() const { return elem; }
-    AP_tree *node() const { return tree_node; }
-    GBDATA *species() const { return gb_species; }
-
-    bool is_text() const { return elem && elem->is_text(); }
-    bool is_line() const { return elem && elem->is_line(); }
-    bool is_branch() const { return branch; }
-    bool is_ruler() const { return ruler; }
-
-    double get_rel_attach() const {
-        // return [0..1] according to exact position where element is dropped
-        if (is_line() && (is_branch() || ruler)) return elem->get_rel_pos();
-        return 0.5; // act like "drop on branch-center"
-    }
-};
-
-AWT_graphic_tree *NT_generate_tree(AW_root *root, GBDATA *gb_main, AD_map_viewer_cb map_viewer_cb);
-bool AWT_show_branch_remark(AW_device *device, const char *remark_branch, bool is_leaf, AW_pos x, AW_pos y, AW_pos alignment, AW_bitset filteri);
-
-#else
-#error TreeDisplay.hxx included twice
-#endif // TREEDISPLAY_HXX

SL/TREEDISP/irstree_display.cxx

-// =============================================================== //
-//                                                                 //
-//   File      : irstree_display.cxx                               //
-//   Purpose   :                                                   //
-//                                                                 //
-//   Institute of Microbiology (Technical University Munich)       //
-//   http://www.arb-home.de/                                       //
-//                                                                 //
-// =============================================================== //
-
-#include "TreeDisplay.hxx"
-
-#include <nds.h>
-
-using namespace AW;
-
-// *********************** paint sub tree ************************
-
-const int tipBoxSize = 3;
-
-struct IRS_data {
-    bool   draw_separator;
-    AW_pos y;
-    AW_pos min_y;    // ypos of folding line
-    AW_pos max_y;
-    AW_pos step_y;
-    AW_pos halfstep_y;
-    AW_pos onePixel;
-    AW_pos fold_x1, fold_x2;
-
-    int    group_closed;
-    double x_scale;
-
-    Vector adjust_text;
-    AW_pos tree_depth;
-
-    AW_pos gap; // between group frame and (box or text)
-    AW_pos openGroupExtra; // extra y-size of unfolded groups
-
-    AW_bitset sep_filter;
-    
-    bool is_size_device;
-
-    void draw_top_separator_once(AW_device *device) {
-        if (draw_separator) {
-            if (!is_size_device) {
-                device->set_line_attributes(AWT_GC_GROUPS, 4, AW_SOLID);
-                device->line(AWT_GC_GROUPS, fold_x1, min_y, fold_x2, min_y, sep_filter);
-            }
-            draw_separator = false;
-        }
-    }
-
-    
-};
-static IRS_data IRS;
-
-AW_pos AWT_graphic_tree::paint_irs_sub_tree(AP_tree *node, AW_pos x_offset) {
-    if (!IRS.is_size_device) {
-        // check clipping rectangle
-        if (IRS.y > IRS.max_y) {
-            return IRS.max_y;
-        }
-        AW_pos height_of_subtree = IRS.step_y*node->gr.view_sum;
-        if (IRS.y + height_of_subtree < IRS.min_y) {
-            IRS.y += height_of_subtree;
-            return IRS.min_y;
-        }
-    }
-
-    if (node->is_leaf) {
-        IRS.y+=IRS.step_y;
-        IRS.draw_top_separator_once(disp_device);
-
-        Position leaf(x_offset, IRS.y);
-
-        if (node->hasName(species_name)) {
-            cursor = leaf;
-            if (IRS.is_size_device) {
-                // hack to fix calculated cursor position:
-                // - IRS tree reports different cursor positions in AW_SIZE and normal draw modes.
-                // - the main reason for the difference is the number of open groups clipped away
-                //   above the separator line.
-                // - There is still some unhandled difference mostlikely caused by the number of
-                //   open groups on the screen, but in most cases the cursor position is inside view now.
-                
-                double correctionPerGroup = IRS.openGroupExtra; // depends on size of marked-species-font
-                double cursorCorrection   = -IRS.group_closed * correctionPerGroup;
-                cursor.movey(cursorCorrection);
-            }
-        }
-
-        AW_click_cd cd(disp_device, (AW_CL)node);
-        
-        int gc = node->gr.gc;
-        if (node->gb_node && GB_read_flag(node->gb_node)) {
-            set_line_attributes_for(node);
-            filled_box(gc, leaf, NT_BOX_WIDTH);
-        }
-
-        Position    textpos  = leaf+IRS.adjust_text;
-        const char *specinfo = make_node_text_nds(gb_main, node->gb_node, NDS_OUTPUT_LEAFTEXT, node, tree_static->get_tree_name());
-        disp_device->text(gc, specinfo, textpos);
-
-        return IRS.y;
-    }
-
-    const char *group_name  = NULL;
-    AW_pos      frame_width = -1;
-
-    if (node->gb_node) {
-        if (!node->father) { // root node - don't try to get taxonomy
-            group_name = tree_static->get_tree_name();
-        }
-        else {
-            group_name = make_node_text_nds(gb_main, node->gb_node, NDS_OUTPUT_LEAFTEXT, node, tree_static->get_tree_name());
-        }
-        frame_width = node->gr.max_tree_depth * IRS.x_scale;
-    }
-
-    if (node->gr.grouped) { // folded group
-        AW_pos y_center;
-
-        AW_pos frame_height = node->gr.view_sum * IRS.step_y;
-        AW_pos frame_y1     = IRS.y+IRS.halfstep_y+IRS.gap;
-        AW_pos frame_y2     = frame_y1 + frame_height;
-
-        if (frame_y2 >= IRS.min_y) {
-            if (frame_y1 < IRS.min_y) { // shift folded groups into the folding area (disappears when completely inside)
-                frame_y1  = IRS.min_y;
-                IRS.min_y += IRS.halfstep_y+IRS.gap;
-            }
-
-            AW_pos    visible_frame_height = frame_y2-frame_y1;
-            Rectangle frame(Position(x_offset, frame_y1), Vector(frame_width, visible_frame_height));
-
-            // draw group frame (unclosed on right hand):
-            AW_click_cd cd(disp_device, (AW_CL)node);
-
-            int gc = AWT_GC_GROUPS;
-            disp_device->set_line_attributes(gc, 1, AW_SOLID);
-            disp_device->line(gc, frame.upper_edge());
-            disp_device->line(gc, frame.left_edge());
-            disp_device->line(gc, frame.lower_edge());
-
-            gc = node->gr.gc;
-            disp_device->set_grey_level(gc, grey_level);
-            set_line_attributes_for(node);
-            filled_box(gc, frame.upper_left_corner(), tipBoxSize);
-
-            Vector    frame2box(IRS.gap, IRS.gap);
-            Rectangle gbox(frame.upper_left_corner()+frame2box, Vector(frame.width()*.5, frame.height()-2*IRS.gap));
-
-            disp_device->box(gc, true, gbox);
-
-            Position box_rcenter = gbox.right_edge().centroid();
-
-            if (group_name) { //  a node name should be displayed
-                const char *groupinfo = GBS_global_string("%s (%u)", group_name, node->gr.leaf_sum);
-                disp_device->text(gc, groupinfo, box_rcenter+IRS.adjust_text);
-            }
-
-            IRS.draw_top_separator_once(disp_device);
-
-            IRS.y    += frame_height + 2*IRS.gap;
-            y_center  = box_rcenter.ypos();
-        }
-        else {
-            IRS.y    += frame_height + 2*IRS.gap;
-            y_center  = IRS.min_y;
-
-            if (IRS.y > IRS.min_y) {
-                IRS.y = IRS.min_y;
-            }
-        }
-        return y_center;
-    }
-
-    AW_pos group_y1 = IRS.y;
-
-    if (group_name != NULL) { // unfolded group
-        if (group_y1 >= IRS.min_y) {
-            IRS.draw_top_separator_once(disp_device);
-            group_y1 = IRS.y + IRS.halfstep_y+IRS.gap;
-        }
-        else {
-            group_y1   = IRS.min_y;
-            IRS.min_y += IRS.openGroupExtra;
-        }
-        IRS.y += IRS.openGroupExtra;
-
-        int         gc = AWT_GC_GROUPS;
-        AW_click_cd cd(disp_device, (AW_CL)node);
-        disp_device->set_line_attributes(gc, 1, AW_DOTTED);
-        disp_device->line(gc, x_offset-IRS.onePixel, group_y1, x_offset+frame_width, group_y1); // opened-group-frame
-
-        const char *groupinfo = GBS_global_string("%s (%u)", group_name, node->gr.leaf_sum);
-        disp_device->text(node->gr.gc, groupinfo, x_offset-IRS.onePixel + IRS.gap, group_y1 + 2*IRS.adjust_text.y() + IRS.gap);
-    }
-
-    // draw subtrees
-    AW_pos left_x = x_offset + IRS.x_scale * node->leftlen;
-    AW_pos left_y = paint_irs_sub_tree(node->get_leftson(), left_x);
-
-    AW_pos right_x = x_offset + IRS.x_scale * node->rightlen;
-    AW_pos right_y = paint_irs_sub_tree(node->get_rightson(), right_x);
-
-    if (group_name != NULL) IRS.group_closed++;
-
-    // draw structure
-    if (left_y > IRS.min_y) {
-        if (left_y < IRS.max_y) { // clip y on top border
-            AW_click_cd cd(disp_device, (AW_CL)node->leftson);
-            if (node->leftson->get_remark()) {
-                AWT_show_branch_remark(disp_device, node->leftson->get_remark(), node->leftson->is_leaf, left_x, left_y, 1, remark_text_filter);
-            }
-            set_line_attributes_for(node->get_leftson()); 
-            draw_branch_line(node->get_leftson()->gr.gc, Position(x_offset, left_y), Position(left_x, left_y), line_filter);
-        }
-    }
-    else {
-        left_y = IRS.min_y;
-    }
-
-    AW_pos y_center = (left_y + right_y)*0.5;
-
-    if (right_y > IRS.min_y && right_y < IRS.max_y) { // visible right branch in lower part of display
-        AW_click_cd cd(disp_device, (AW_CL)node->rightson);
-        if (node->rightson->get_remark()) {
-            AWT_show_branch_remark(disp_device, node->rightson->get_remark(), node->rightson->is_leaf, right_x, right_y, 1, remark_text_filter);
-        }
-        set_line_attributes_for(node->get_rightson()); 
-        draw_branch_line(node->get_rightson()->gr.gc, Position(x_offset, right_y), Position(right_x,  right_y), line_filter);
-    }
-
-    AW_click_cd cd(disp_device, (AW_CL)node);
-    set_line_attributes_for(node->get_leftson());
-    disp_device->line(node->get_leftson()->gr.gc, x_offset, y_center, x_offset, left_y);
-
-    set_line_attributes_for(node->get_rightson());
-    disp_device->line(node->get_rightson()->gr.gc, x_offset, y_center, x_offset, right_y);
-
-    if (group_name != NULL) { // close unfolded group brackets and draw tipbox
-        IRS.y  += IRS.halfstep_y+IRS.gap;
-
-        int gc = AWT_GC_GROUPS;
-        disp_device->set_line_attributes(gc, 1, AW_DOTTED);
-        disp_device->line(gc, x_offset-IRS.onePixel, IRS.y, x_offset+frame_width, IRS.y); // opened-group-frame
-        disp_device->line(gc, x_offset-IRS.onePixel, group_y1, x_offset-IRS.onePixel,  IRS.y); // opened-group-frame
-        
-        gc = node->gr.gc;
-        disp_device->set_grey_level(gc, grey_level);
-        set_line_attributes_for(node);
-        filled_box(gc, Position(x_offset-IRS.onePixel, group_y1), tipBoxSize);
-    }
-    return y_center;
-}
-
-void AWT_graphic_tree::show_irs_tree(AP_tree *at, double height) {
-
-    IRS.draw_separator = true;
-    IRS.y              = 0;
-    IRS.step_y         = height;
-    IRS.halfstep_y     = IRS.step_y*0.5;
-    IRS.x_scale        = 200.0;      // @@@ should not have any effect, since display gets x-scaled. But if it's to low (e.g. 1.0) scaling on zoom-reset does not work
-
-    const AW_font_limits& limits = disp_device->get_font_limits(AWT_GC_SELECTED, 0);
-
-    IRS.adjust_text    = disp_device->rtransform(Vector(NT_BOX_WIDTH, limits.ascent*0.5));
-    IRS.onePixel       = disp_device->rtransform_size(1.0);
-    IRS.gap            = 3*IRS.onePixel;
-    IRS.group_closed   = 0;
-    IRS.tree_depth     = at->gr.max_tree_depth;
-    IRS.openGroupExtra = IRS.step_y+IRS.gap;
-    IRS.sep_filter     = AW_SCREEN|AW_PRINTER_CLIP;
-
-    IRS.is_size_device = disp_device->type() == AW_DEVICE_SIZE;
-
-    Position  corner = disp_device->rtransform(Origin);   // real world coordinates of left/upper screen corner
-    Rectangle rclip  = disp_device->get_rtransformed_cliprect();
-
-    // the following values currently contain nonsense for size device @@@
-    IRS.min_y   = corner.ypos();
-    IRS.max_y   = rclip.bottom();
-    IRS.fold_x1 = rclip.left();
-    IRS.fold_x2 = rclip.right();
-
-    list_tree_ruler_y           = paint_irs_sub_tree(at, 0);
-    irs_tree_ruler_scale_factor = IRS.x_scale;
-    
-    disp_device->invisible(corner); // @@@ remove when size-dev works
-}

SL/TREEDISP/needs_libs

-# libraries needed to link against SL/TREEDISP/TREEDISP.a
-
-SL/AP_TREE/AP_TREE.a
-SL/NDS/NDS.a

SL/TREE_ADMIN/Makefile

-# for variables passed from parent makefile see ../../SOURCE_TOOLS/parent_make.txt
-
-.SUFFIXES: .o .cxx .depend
-
-OBJECTS=$(subst .cxx,.o,$(wildcard *.cxx))
-
-$(MAIN): $(OBJECTS)
-	$(LINK_STATIC_LIB) $(MAIN) $(OBJECTS)
-
-.cxx.o:
-	$(A_CXX) $(cflags) $(cxxflags) -c $< $(CXX_INCLUDES) $(POST_COMPILE)
-
-clean:
-	rm -f $(OBJECTS) *.a
-
-DEPENDS = $(OBJECTS:.o=.depend)
-depends: $(DEPENDS)
-	@cat $(DEPENDS) | grep -v '^#' >>Makefile
-	@rm $(DEPENDS)
-$(DEPENDS): depend.init
-depend.init:
-	$(MAKEDEPEND) $(MAKEDEPENDFLAGS) 2>/dev/null # remove dependencies
-.c.depend:
-	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
-.cxx.depend:
-	$(MAKEDEPEND) -f- $(MAKEDEPENDFLAGS) $< 2>/dev/null >$@
-
-# DO NOT DELETE
-
-# Do not add dependencies manually - use 'make depend' in $ARBHOME
-# For formatting issues see SOURCE_TOOLS/fix_depends.pl (from SL)
-
-TreeAdmin.o: TreeAdmin.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/ad_prot.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/ad_t_prot.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arb_assert.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arb_core.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arb_error.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arb_global_defs.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arb_msg.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arb_strbuf.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arb_string.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arbdb.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arbdb_base.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arbdbt.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/arbtools.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/attributes.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/aw_awar.hxx
-TreeAdmin.o: $(ARBHOME)/INCLUDE/aw_base.hxx
-TreeAdmin.o: $(ARBHOME)/INCLUDE/aw_keysym.hxx
-TreeAdmin.o: $(ARBHOME)/INCLUDE/aw_msg.hxx
-TreeAdmin.o: $(ARBHOME)/INCLUDE/aw_root.hxx
-TreeAdmin.o: $(ARBHOME)/INCLUDE/aw_window.hxx
-TreeAdmin.o: $(ARBHOME)/INCLUDE/awt_TreeAwars.hxx
-TreeAdmin.o: $(ARBHOME)/INCLUDE/cb.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/cb_base.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/cbtypes.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/cxxforward.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/downcast.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/dupstr.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/gccver.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/smartptr.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/static_assert.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/test_global.h
-TreeAdmin.o: $(ARBHOME)/INCLUDE/ttypes.h

SL/TREE_ADMIN/TreeAdmin.cxx

-// ============================================================= //
-//                                                               //
-//   File      : TreeAdmin.cxx                                   //
-//   Purpose   : Common tree admin functionality                 //
-//                                                               //
-//   Coded by Ralf Westram (coder@reallysoft.de) in April 2012   //
-//   Institute of Microbiology (Technical University Munich)     //
-//   http://www.arb-home.de/                                     //
-//                                                               //
-// ============================================================= //
-
-#include "TreeAdmin.h"
-#include <aw_window.hxx>
-#include <aw_root.hxx>
-#include <aw_awar.hxx>
-#include <arbdbt.h>
-#include <arb_strbuf.h>
-#include <cctype>
-#include <aw_msg.hxx>
-#include <arb_global_defs.h>
-#include <awt_TreeAwars.hxx>
-
-#define ta_assert(cond) arb_assert(cond)
-
-#define AWAR_TREE_SOURCE "tmp/ad_tree/tree_source"
-#define AWAR_TREE_DEST   "tmp/ad_tree/tree_dest"
-
-namespace TreeAdmin {
-
-    void create_awars(AW_root *root, AW_default aw_def, bool registerTreeAwar) {
-        AW_awar *awar_srcTree = root->awar_string(AWAR_TREE_SOURCE, 0, aw_def)->set_srt(GBT_TREE_AWAR_SRT);
-        if (registerTreeAwar) AWT_registerTreeAwarSimple(awar_srcTree);
-        root->awar_string(AWAR_TREE_DEST, 0, aw_def)->set_srt(GBT_TREE_AWAR_SRT); // no need to register (awar always follows the tree selected in admin window!)
-    }
-    AW_awar *source_tree_awar(AW_root *root) {
-        return root->awar(AWAR_TREE_SOURCE);
-    }
-    AW_awar *dest_tree_awar(AW_root *root) {
-        return root->awar(AWAR_TREE_DEST);
-    }
-
-    AW_awar *Spec::tree_awar(AW_root *awr) const {
-        return awr->awar(awar_selected_tree);
-    }
-
-    void delete_tree_cb(AW_window *aww, const Spec *spec) {
-        AW_awar    *awar_tree = spec->tree_awar(aww->get_root());
-        char       *name      = awar_tree->read_string();
-        GBDATA     *gb_main   = spec->get_gb_main();
-        GB_ERROR    error     = NULL;
-        GBDATA     *gb_tree;
-
-        // 1. TA: switch to next tree
-        {
-            GB_transaction ta(gb_main);
-            gb_tree = GBT_find_tree(gb_main, name);
-            if (!gb_tree) error = "Please select tree to delete";
-            else {
-                AWT_announce_tree_deleted(name);
-                GBDATA *gb_next = GBT_find_next_tree(gb_tree);
-                awar_tree->write_string(gb_next ? GBT_get_tree_name(gb_next) : NO_TREE_SELECTED);
-            }
-            error = ta.close(error);
-        }
-
-        // 2. TA: delete old tree
-        if (!error) {
-            GB_transaction ta(gb_main);
-            error = GB_delete(gb_tree);
-            error = ta.close(error);
-        }
-
-        if (error) {
-            aw_message(error);
-            awar_tree->write_string(name); // switch back to failed tree
-        }
-
-        free(name);
-    }
-    
-    static GB_ERROR tree_append_remark(GBDATA *gb_tree, const char *add_to_remark) {
-        GB_ERROR  error       = 0;
-        GBDATA   *gb_remark   = GB_search(gb_tree, "remark", GB_STRING);
-        if (!gb_remark) error = GB_await_error();
-        else {
-            char *old_remark       = GB_read_string(gb_remark);
-            if (!old_remark) error = GB_await_error();
-            else {
-                GBS_strstruct *new_remark = GBS_stropen(2000);
-
-                GBS_strcat(new_remark, old_remark);
-                GBS_chrcat(new_remark, '\n');
-                GBS_strcat(new_remark, add_to_remark);
-
-                error = GB_write_string(gb_remark, GBS_mempntr(new_remark));
-
-                GBS_strforget(new_remark);
-            }
-            free(old_remark);
-        }
-        return error;
-    }
-
-    static void tree_copy_or_rename_cb(AW_window *aww, bool do_copy, const Spec& spec) {
-        AW_root  *aw_root   = aww->get_root();
-        AW_awar  *awar_tree = spec.tree_awar(aw_root);
-        char     *source    = awar_tree->read_string();
-        char     *dest      = aw_root->awar(AWAR_TREE_DEST)->read_string();
-        GB_ERROR  error     = NULL;
-
-        if (!error && !dest[0]) error = "Please enter new tree name";
-        if (!error) {
-            GBDATA *gb_main = spec.get_gb_main();
-            error           = GB_begin_transaction(gb_main);
-            if (!error) {
-                if (do_copy) {
-                    error = GBT_copy_tree(gb_main, source, dest);
-                    if (!error) {
-                        GBDATA *gb_new_tree = GBT_find_tree(gb_main, dest);
-                        ta_assert(gb_new_tree);
-                        error = tree_append_remark(gb_new_tree, GBS_global_string("[created as copy of '%s']", source));
-                    }
-                }
-                else {
-                    error = GBT_rename_tree(gb_main, source, dest);
-                    if (!error) AWT_announce_tree_renamed(source, dest);
-                }
-            }
-
-            if (!error) awar_tree->write_string(dest);
-            error = GB_end_transaction(gb_main, error);
-        }
-
-        aww->hide_or_notify(error);
-
-        free(dest);
-        free(source);
-    }
-
-    static void tree_rename_cb(AW_window *aww, const Spec *spec) { tree_copy_or_rename_cb(aww, false, *spec); }
-    static void tree_copy_cb  (AW_window *aww, const Spec *spec) { tree_copy_or_rename_cb(aww, true, *spec);  }
-
-    static void current_as_dest_treename_cb(AW_window *aww, const Spec *spec) {
-        AW_root    *awr  = aww->get_root();
-        dest_tree_awar(awr)->write_string(spec->tree_awar(awr)->read_char_pntr());
-    }
-
-    static void make_dest_treename_unique_cb(AW_window *aww, const Spec *spec) {
-        // generated a unique treename
-        AW_root *awr       = aww->get_root();
-        AW_awar *awar_dest = awr->awar(AWAR_TREE_DEST);
-
-        char *name = awar_dest->read_string();
-        int   len  = strlen(name);
-
-        for (int p = len-1; p >= 0; --p) {
-            bool auto_modified = isdigit(name[p]) || name[p] == '_';
-            if (!auto_modified) break;
-            name[p] = 0;
-        }
-
-        {
-            GBDATA         *gb_main = spec->get_gb_main();
-            GB_transaction  ta(gb_main);
-
-            if (!GBT_find_tree(gb_main, name)) {
-                awar_dest->write_string("");
-                awar_dest->write_string(name);
-            }
-            else {
-                for (int i = 2; ; i++) {
-                    const char *testName = GBS_global_string("%s_%i", name, i);
-                    if (!GBT_find_tree(gb_main, testName)) { // found unique name
-                        awar_dest->write_string(testName);
-                        break;
-                    }
-                }
-            }
-        }
-
-        free(name);
-    }
-
-    static AW_window *create_copy_or_rename_window(AW_root *root, const char *win_id, const char *win_title, const char *go_label, void (*go_cb)(AW_window*, const Spec*), const Spec *spec) {
-        AW_window_simple *aws = new AW_window_simple;
-        aws->init(root, win_id, win_title);
-
-        aws->at(10, 10);
-        aws->auto_space(10, 10);
-
-        aws->at_newline();
-        aws->label("Current:");
-        aws->callback(makeWindowCallback(current_as_dest_treename_cb, spec));
-        aws->at_set_to(true, false, -10, 25);
-        aws->create_button("use_current", spec->tree_awar(aws->get_root())->awar_name);
-
-        aws->at_newline();
-        aws->label("New:    ");
-        aws->at_set_to(true, false, -10, 30);
-        aws->create_input_field(AWAR_TREE_DEST);
-
-        aws->at_newline();
-        aws->callback(makeWindowCallback(go_cb, spec));
-        aws->create_autosize_button("GO", go_label, "");
-
-        aws->callback((AW_CB0)AW_POPDOWN);
-        aws->create_autosize_button("CLOSE", "Abort", "A");
-
-        aws->callback(makeWindowCallback(make_dest_treename_unique_cb, spec));
-        aws->create_autosize_button("UNIQUE", "Unique name", "U");
-    
-        aws->at_newline();
-
-        return aws;
-    }
-
-    
-    AW_window *create_rename_window(AW_root *root, const Spec *spec) {
-        return create_copy_or_rename_window(root, "RENAME_TREE", "Rename Tree", "Rename Tree", tree_rename_cb, spec);
-    }
-    AW_window *create_copy_window(AW_root *root, const Spec *spec) {
-        return create_copy_or_rename_window(root, "COPY_TREE",   "Copy Tree",   "Copy Tree",   tree_copy_cb, spec);
-    }
-
-    
-};
-

SL/TREE_ADMIN/TreeAdmin.h

-// ============================================================= //
-//                                                               //
-//   File      : TreeAdmin.h                                     //
-//   Purpose   : Common tree admin functionality                 //
-//                                                               //
-//   Coded by Ralf Westram (coder@reallysoft.de) in April 2012   //
-//   Institute of Microbiology (Technical University Munich)     //
-//   http://www.arb-home.de/                                     //
-//                                                               //
-// ============================================================= //
-
-#ifndef TREEADMIN_H
-#define TREEADMIN_H
-
-#ifndef AW_BASE_HXX
-#include <aw_base.hxx>
-#endif
-
-class AW_awar;
-
-namespace TreeAdmin {
-
-    class Spec {
-        GBDATA     *gb_main;
-        const char *awar_selected_tree;
-    public:
-        Spec(GBDATA *gb_main_, const char *awar_selected_tree_)
-            : gb_main(gb_main_),
-              awar_selected_tree(awar_selected_tree_)
-        {}
-
-        GBDATA *get_gb_main() const { return gb_main; }
-        AW_awar *tree_awar(AW_root *awr) const;
-    };
-
-    void create_awars(AW_root *root, AW_default aw_def, bool registerTreeAwar);
-    AW_awar *dest_tree_awar(AW_root *root);
-    AW_awar *source_tree_awar(AW_root *root);
-
-    AW_window *create_rename_window(AW_root *root, const Spec *spec);
-    AW_window *create_copy_window(AW_root *root, const Spec *spec);
-
-    void delete_tree_cb(AW_window *aww, const Spec *spec);
-};
-
-#else
-#error TreeAdmin.h included twice
-#endif // TREEADMIN_H