New upstream version 17.0.1+dfsg

<?xml version="1.0" encoding="UTF-8"?>

<classpath>

	<classpathentry kind="src" path="corba"/>

	<classpathentry kind="src" path="lib"/>

	<classpathentry including="nsdb/|seqdb/|type/" kind="src" path="ant-build/src/main"/>

	<classpathentry excluding="ant-build/src/main/|uk/ac/sanger/artemis/ExternalProgramUtils.java" including="nsdb/|org/|seqdb/|type/|uk/" kind="src" path=""/>

	<classpathentry excluding="ant-build|cobertura-lib|coverage-report|data|docs|evosuite-dependencies|evosuite-libs|evosuite-tests|jacoco-lib|lib|evosuite-tests/" including="uk/**" kind="src" output="eclipse-classes" path="test"/>

	<classpathentry including="uk/**" kind="src" output="eclipse-classes" path="test/evosuite-tests"/>

	<classpathentry excluding="main/" kind="src" path="ant-build/src"/>

	<classpathentry excluding="ant-build/classes/|ant-build/src/|docs|test|test/evosuite-tests/|uk/ac/sanger/artemis/ExternalProgramUtils.java" including="org/|uk/" kind="src" path=""/>

	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>

	<classpathentry kind="lib" path="lib/jemAlign.jar"/>

	<classpathentry kind="lib" path="lib/jakarta-regexp-1.2.jar"/>

	<classpathentry kind="lib" path="lib/ibatis/ibatis-2.3.4.726.jar"/>

	<classpathentry kind="lib" path="lib/ibatis/log4j-1.2.14.jar"/>

	<classpathentry kind="lib" path="lib/postgresql-8.4-701.jdbc3.jar"/>

	<classpathentry kind="lib" path="lib/picard/picard.jar"/>

	<classpathentry kind="lib" path="lib/picard/sam.jar"/>

	<classpathentry kind="lib" path="lib/commons-net-2.2.jar"/>

	<classpathentry kind="lib" path="lib/batik/batik-awt-util.jar"/>

	<classpathentry kind="lib" path="lib/batik/batik-codec.jar"/>

	<classpathentry kind="lib" path="lib/batik/batik-dom.jar"/>

	<classpathentry kind="lib" path="lib/batik/batik-util.jar"/>

	<classpathentry kind="lib" path="lib/batik/batik-xml.jar"/>

	<classpathentry kind="lib" path="lib/commons-lang-2.6.jar"/>

	<classpathentry kind="output" path="ant-build/classes/main"/>

	<classpathentry kind="lib" path="test/lib/junit-4.11.jar"/>

	<classpathentry kind="lib" path="/Users/kp11/workspace/applications/Artemis/eclipse-classes"/>

	<classpathentry kind="lib" path="test/evosuite-lib/evosuite-1.0.5.jar"/>

	<classpathentry kind="lib" path="lib/commons-net-3.6.jar"/>

	<classpathentry kind="lib" path="lib/picard/picard.jar"/>

	<classpathentry kind="output" path="eclipse-classes"/>

</classpath>

*.class

.settings

ant-build

test/ant-build

**/.DS_Store

**/*.log

test/coverage-report

jar_build

tar_build

artemis_compiled.tar

/eclipse-classes/

/test-kjp/

language: java

jdk:

  - openjdk7

  - openjdk6

  - oraclejdk7

  - openjdk8

  - oraclejdk8

sudo: false

env:

  global:

    - BUILD_CMD='make'

    - RUN_TESTS=false

matrix:

  include:

    - jdk: openjdk7

      env: BUILD_CMD='ant -f build.xml'

    - jdk: oraclejdk8

      env: 

        - BUILD_CMD='ant -f build.xml'

        - RUN_TESTS=true

cache:

  directories:

  - "${HOME}/dependencies"

  - "source install_dependencies.sh"

install:

  - "$BUILD_CMD"

  - "cd test"

  - "ln -s $(pwd)/../etc/log4j.properties ."

script: ant -f build-test.xml test -DEMBOSS_ROOT=$EMBOSS_ROOT | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ]

script:

  - if [ "$RUN_TESTS" == "true" ]; then

      cd test;

      ln -s $(pwd)/../etc/log4j.properties .;

      ./RunDefaultUnitTests.sh | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ];

    fi

Tim Carver (path-help@sanger.ac.uk)

Sascha Steinbiss (path-help@sanger.ac.uk)

Kim Rutherford (path-help@sanger.ac.uk)

Kevin Pepper (path-help@sanger.ac.uk)

Version 17

	Artemis/ACT and associated applications have been upgraded to Java 8. Java 7/6/5 are now no longer supported - RT ticket #589103

	BamView fixes/changes - 

		1) Improved mouse selection of reads.

		2) Fixed exceptions thrown when zooming into an area with secondary reads or SNPs enabled - RT ticket #596489: Problem zooming in using isoseq data

		3) Removed Samtools (htsjdk) jar and updated Picard jar (which includes htsjdk).

		4) Upgraded Apache Commons Net jar - used for ftp'ing. 

		5) Added Cram file loading and fixed defects around that code area (also related RT ticket #560982: Artemis fails to build from source).

		6) Added display of bam secondary & supplementary alignment flags to read details pop-up window.

		7) Improved error handling/reporting, although this still needs more work.

		8) Added buffer sizing to FTPSeekableStream.

		9) Performance tweak for BAM file indexing.

		10) Fixed issue in BamView whereby if you went to the end of a long contig and then switched to a shorter one (via the combo), you would end up off the end of the sequence

			resulting in a negative array index exception. Code has been changed to reset display to the start of sequence when the combo is changed (i.e. same as Artemis).

		11) Added bamview_perform_detailed_validation boolean property that can be set to perform more detailed sam validation during loading - this can be slow for large files.

	Added EvoSuite unit tests and additional targeted tests (RT ticket #419534: Develop a test suite for Artemis).

	Added Jacoco unit test coverage reporting - manual tests only currently. This may be switched to Clover in the future if this proves compatible with EvoSuite

		- for the moment we are stuck with two coverage reports - evosuite and Jacoco.

	Removed redundant Corba libraries.

	Upgraded JUnit jar.

	Changed Travis yml build file. RT ticket #597497: Set up artemis tests to run on travis build.

	Changed all build scripts and startup scripts - RT ticket #598617. Removed building of artemis_mac.jar which is not used. 

	Removed etc/gene_builder script and the gff2embl script (and documentation references) - no longer supported. 

	Fixed RT ticket #606061 - Using EBI-Dbfetch on ARTEMIS. Change to DbfetchEntrySource.java due to incorrect regular expression and EBI URL.

	Resized splash screen, as it was too small to the accommodate text info.

	Updated splash screen logo.

	Added error handling for dnaplotter template file loading in standalone mode.

	Bioconda recipe prep work - RT ticket #341139.

	Fixed RT ticket #467433 - Genbank DBSOURCE field was not recognised by Artemis. DBLINK was already added.

	Fixed RT ticket #503254 - Act doesn't detect if file does not exist.

	KNOWN ISSUES: 

		1) Java JDKs 1.8.0_131 and above have a Swing bug related to overlaying of modal dialogs for Mac OS X: https://bugs.openjdk.java.net/browse/JDK-8179335

		2) There is a current bug in htsjdk whereby calls to the queryMate functionality can throw an exception on reads with secondaries and/or supplementals. 

		   This affects looking up properties for a selected read on bamview - https://github.com/samtools/htsjdk/issues/1065

Version 16

	Add 'Features Within Selection' option to the 'Select' menu to select

	features that are contained by a selected base range.