Commit a057cc90 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 6.0.6

parent 610f06bb

SL/TRANSLATE/Makefile

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# 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

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// =============================================================== //

//                                                                 //

//   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/Translate.hxx

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// =============================================================== //

//                                                                 //

//   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/                                       //

//                                                                 //

// =============================================================== //



#ifndef TRANSLATE_HXX

#define TRANSLATE_HXX



#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);



#else

#error Translate.hxx included twice

#endif // TRANSLATE_HXX

SL/TRANSLATE/needs_libs

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



SL/PRONUC/PRONUC.a

SL/TREEDISP/Makefile

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# 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