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in repository malt.
commit 9f97f4f90e86a62d73e128be30595ca6628952f0
Author: Andreas Tille <ti...@debian.org>
Date: Wed May 3 11:48:25 2017 +0200
New upstream version 0.0+20170502
---
antbuild/build.xml | 11 +++++------
installer/malt.install4j | 14 +++++++-------
src/malt/MaltBuild.java | 2 +-
src/malt/MaltRun.java | 4 ++--
src/malt/io/RMA6Writer.java | 6 ++++--
tex/manual/manual.pdf | Bin 202539 -> 202615 bytes
tex/manual/manual.tex | 18 +++++++++---------
tex/manual/versioninfo.tex | 2 +-
tex/manual/versioninfo_new.tex | 2 +-
tex/manual/versioninfo_old.tex | 2 +-
10 files changed, 31 insertions(+), 30 deletions(-)
diff --git a/antbuild/build.xml b/antbuild/build.xml
index f8d9724..69922c6 100644
--- a/antbuild/build.xml
+++ b/antbuild/build.xml
@@ -32,17 +32,16 @@
<!-- copy resources -->
<target name="copy_resources" depends="init">
<copy todir="${classDir}/resources">
- <fileset dir="../resources" excludes=".svn/**"/>
+ <fileset dir="../resources"/>
</copy>
</target>
<!-- copy sources -->
<target name="copy_sources" depends="copy_resources">
<copy todir="${srcDir}">
- <fileset dir="${jlodaSrcDir}"
- excludes=".svn/** jloda/matrix/** jloda/models/** test/**
bioinf1/** gbi/** gitter/**"/>
- <fileset dir="${meganSrcDir}" excludes=".svn/** test/** malt/**"/>
- <fileset dir="${maltSrcDir}" excludes=".svn/** test/**"/>
+ <fileset dir="${jlodaSrcDir}" excludes="com/apple/**"/>
+ <fileset dir="${meganSrcDir}"/>
+ <fileset dir="${maltSrcDir}"/>
</copy>
</target>
@@ -87,7 +86,7 @@
<!-- removes all that has been built -->
<target name="clean">
<delete dir="${classDir}" includeEmptyDirs="true"/>
- <delete dir="src" includeEmptyDirs="true"/>
+ <delete dir="${srcDir}" includeEmptyDirs="true"/>
<delete file="MALT.jar"/>
</target>
</project>
diff --git a/installer/malt.install4j b/installer/malt.install4j
index 8835a82..b4ec5da 100644
--- a/installer/malt.install4j
+++ b/installer/malt.install4j
@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
-<install4j version="6.1.1" transformSequenceNumber="5">
+<install4j version="6.1.3" transformSequenceNumber="5">
<directoryPresets config="../../megan6/jars/data.jar" />
<application name="MALT" distributionSourceDir=""
applicationId="3229-5251-7410-5330" mediaDir="../../../builds"
mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}"
compression="6" lzmaCompression="false" pack200Compression="false"
excludeSignedFromPacking="true" commonExternalFiles="false"
createMd5Sums="true" shrinkRuntime="true" shortName="MALT" publisher="Daniel
Huson's Lab, University of Tuebingen" publisherWeb="www-ab.informatik.uni-tuebi
[...]
<languages skipLanguageSelection="false"
languageSelectionInPrincipalLanguage="false">
@@ -73,7 +73,7 @@
</components>
</files>
<launchers>
- <launcher name="malt-build-gui" id="1691242235" customizedId=""
external="false" excludeFromMenu="false" unixMode="755" menuName=""
icnsFile="../resources/icons/malt-build.icns" customMacBundleIdentifier="false"
macBundleIdentifier="" swtApp="false" fileset=""
macBundleBinary="JavaApplicationStub" addMacEntitlements="false"
macEntitlementsFile="" useCustomMacosExecutableName="false"
customMacosExecutableName="">
+ <launcher name="malt-build-gui" id="1691242235" customizedId=""
external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true"
menuName="" icnsFile="../resources/icons/malt-build.icns"
customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false"
fileset="" macBundleBinary="JavaApplicationStub" addMacEntitlements="false"
macEntitlementsFile="" useCustomMacosExecutableName="false"
customMacosExecutableName="" useJavaMinVersionOverride="false"
javaMinVersionOver [...]
<executable name="malt-build-gui" type="1" iconSet="true" iconFile=""
executableDir="" redirectStderr="true" stderrFile="malt-build.log"
stderrMode="overwrite" redirectStdout="true" stdoutFile="malt-build.log"
stdoutMode="overwrite" failOnStderrOutput="true" executableMode="1"
changeWorkingDirectory="false" workingDirectory="." singleInstance="false"
serviceStartType="2" serviceDependencies="" serviceDescription=""
jreLocation="" executionLevel="asInvoker" checkConsoleParameter="fa [...]
<versionInfo include="false" fileVersion="" fileDescription=""
legalCopyright="" internalName="" productName="" />
</executable>
@@ -108,7 +108,7 @@
<file path="../resources/icons/malt-build48.png" />
</iconImageFiles>
</launcher>
- <launcher name="malt-run-gui" id="1691243093" customizedId=""
external="false" excludeFromMenu="false" unixMode="755" menuName=""
icnsFile="../resources/icons/malt-run.icns" customMacBundleIdentifier="false"
macBundleIdentifier="" swtApp="false" fileset=""
macBundleBinary="JavaApplicationStub" addMacEntitlements="false"
macEntitlementsFile="" useCustomMacosExecutableName="false"
customMacosExecutableName="">
+ <launcher name="malt-run-gui" id="1691243093" customizedId=""
external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true"
menuName="" icnsFile="../resources/icons/malt-run.icns"
customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false"
fileset="" macBundleBinary="JavaApplicationStub" addMacEntitlements="false"
macEntitlementsFile="" useCustomMacosExecutableName="false"
customMacosExecutableName="" useJavaMinVersionOverride="false"
javaMinVersionOverride [...]
<executable name="malt-run-gui" type="1" iconSet="true" iconFile=""
executableDir="" redirectStderr="true" stderrFile="malt-run.log"
stderrMode="overwrite" redirectStdout="true" stdoutFile="malt-run.log"
stdoutMode="overwrite" failOnStderrOutput="true" executableMode="1"
changeWorkingDirectory="false" workingDirectory="." singleInstance="false"
serviceStartType="2" serviceDependencies="" serviceDescription=""
jreLocation="" executionLevel="asInvoker" checkConsoleParameter="false" g [...]
<versionInfo include="false" fileVersion="" fileDescription=""
legalCopyright="" internalName="" productName="" />
</executable>
@@ -143,7 +143,7 @@
<file path="../resources/icons/malt-run48.png" />
</iconImageFiles>
</launcher>
- <launcher name="malt-build" id="1691243204" customizedId=""
external="false" excludeFromMenu="false" unixMode="755" menuName=""
icnsFile="../resources/icons/malt-build.icns" customMacBundleIdentifier="false"
macBundleIdentifier="" swtApp="false" fileset=""
macBundleBinary="JavaApplicationStub" addMacEntitlements="false"
macEntitlementsFile="" useCustomMacosExecutableName="false"
customMacosExecutableName="">
+ <launcher name="malt-build" id="1691243204" customizedId=""
external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true"
menuName="" icnsFile="../resources/icons/malt-build.icns"
customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false"
fileset="" macBundleBinary="JavaApplicationStub" addMacEntitlements="false"
macEntitlementsFile="" useCustomMacosExecutableName="false"
customMacosExecutableName="" useJavaMinVersionOverride="false"
javaMinVersionOverride [...]
<executable name="malt-build" type="1" iconSet="true" iconFile=""
executableDir="" redirectStderr="false" stderrFile="error.log"
stderrMode="overwrite" redirectStdout="false" stdoutFile="output.log"
stdoutMode="overwrite" failOnStderrOutput="true" executableMode="2"
changeWorkingDirectory="false" workingDirectory="." singleInstance="false"
serviceStartType="2" serviceDependencies="" serviceDescription=""
jreLocation="" executionLevel="asInvoker" checkConsoleParameter="false" global
[...]
<versionInfo include="false" fileVersion="" fileDescription=""
legalCopyright="" internalName="" productName="" />
</executable>
@@ -178,7 +178,7 @@
<file path="../resources/icons/malt-build48.png" />
</iconImageFiles>
</launcher>
- <launcher name="malt-run" id="1691243207" customizedId="" external="false"
excludeFromMenu="false" unixMode="755" menuName=""
icnsFile="../resources/icons/malt-run.icns" customMacBundleIdentifier="false"
macBundleIdentifier="" swtApp="false" fileset=""
macBundleBinary="JavaApplicationStub" addMacEntitlements="false"
macEntitlementsFile="" useCustomMacosExecutableName="false"
customMacosExecutableName="">
+ <launcher name="malt-run" id="1691243207" customizedId="" external="false"
excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName=""
icnsFile="../resources/icons/malt-run.icns" customMacBundleIdentifier="false"
macBundleIdentifier="" swtApp="false" fileset=""
macBundleBinary="JavaApplicationStub" addMacEntitlements="false"
macEntitlementsFile="" useCustomMacosExecutableName="false"
customMacosExecutableName="" useJavaMinVersionOverride="false"
javaMinVersionOverride="" [...]
<executable name="malt-run" type="1" iconSet="true" iconFile=""
executableDir="" redirectStderr="false" stderrFile="error.log"
stderrMode="overwrite" redirectStdout="false" stdoutFile="output.log"
stdoutMode="overwrite" failOnStderrOutput="true" executableMode="2"
changeWorkingDirectory="false" workingDirectory="." singleInstance="false"
serviceStartType="2" serviceDependencies="" serviceDescription=""
jreLocation="" executionLevel="asInvoker" checkConsoleParameter="false"
globalSi [...]
<versionInfo include="false" fileVersion="" fileDescription=""
legalCopyright="" internalName="" productName="" />
</executable>
@@ -1461,7 +1461,7 @@
wizardContext.setCancelButtonVisible(false);</preActivation>
<content />
</installerScript>
</unixInstaller>
- <macosFolder name="Mac OS X Folder" id="1691242149" customizedId=""
mediaFileName="" installDir="MALT" overridePrincipalLanguage="true"
jreBitType="all" runPostProcessor="false" postProcessor=""
failOnPostProcessorError="false" useLegacyMediaFileIds="false"
legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false"
includedJRE="macosx-amd64-1.8.0_92" manualJREEntry="false" bundleType="1"
jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="fal
[...]
+ <macosFolder name="Mac OS X Folder" id="1691242149" customizedId=""
mediaFileName="" installDir="MALT" overridePrincipalLanguage="true"
jreBitType="all" runPostProcessor="false" postProcessor=""
failOnPostProcessorError="false" useLegacyMediaFileIds="false"
legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false"
includedJRE="macosx-amd64-1.8.0_112" manualJREEntry="false" bundleType="1"
jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="fa
[...]
<excludedComponents />
<includedDownloadableComponents />
<excludedLaunchers />
@@ -1475,7 +1475,7 @@
wizardContext.setCancelButtonVisible(false);</preActivation>
</autoUpdate>
<topLevelFiles />
</macosFolder>
- <windows name="Windows" id="1691242407" customizedId=""
mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}"
installDir="Malt" overridePrincipalLanguage="true" jreBitType="64"
runPostProcessor="false" postProcessor="" failOnPostProcessorError="false"
useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL=""
includeAllDownloadableComponents="false" includedJRE="windows-amd64-1.8.0_92"
manualJREEntry="false" bundleType="1" jreURL="" jreSha [...]
+ <windows name="Windows" id="1691242407" customizedId=""
mediaFileName="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}"
installDir="Malt" overridePrincipalLanguage="true" jreBitType="64"
runPostProcessor="false" postProcessor="" failOnPostProcessorError="false"
useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL=""
includeAllDownloadableComponents="false" includedJRE="windows-amd64-1.8.0_112"
manualJREEntry="false" bundleType="1" jreURL="" jreSh [...]
<excludedComponents />
<includedDownloadableComponents />
<excludedLaunchers />
diff --git a/src/malt/MaltBuild.java b/src/malt/MaltBuild.java
index db0aaa8..d8e229f 100644
--- a/src/malt/MaltBuild.java
+++ b/src/malt/MaltBuild.java
@@ -85,7 +85,7 @@ public class MaltBuild {
final ArgsOptions options = new ArgsOptions(args,
ProgramProperties.getProgramName(), "MaltBuild", "Builds an index for MALT
(MEGAN alignment tool)");
options.setAuthors("Daniel H. Huson");
options.setVersion(ProgramProperties.getProgramVersion());
- options.setLicense("Copyright (C) 2016 Daniel H. Huson. This program
comes with ABSOLUTELY NO WARRANTY.");
+ options.setLicense("Copyright (C) 2017 Daniel H. Huson. This program
comes with ABSOLUTELY NO WARRANTY.");
options.comment("Input:");
final List<String> inputFiles = options.getOptionMandatory("i",
"input", "Input reference file(s)", new LinkedList<String>());
diff --git a/src/malt/MaltRun.java b/src/malt/MaltRun.java
index 05b3421..8213a2d 100644
--- a/src/malt/MaltRun.java
+++ b/src/malt/MaltRun.java
@@ -110,7 +110,7 @@ public class MaltRun {
final ArgsOptions options = new ArgsOptions(args, this,
ProgramProperties.getProgramName(), "Aligns sequences using MALT (MEGAN
alignment tool)");
options.setAuthors("Daniel H. Huson");
options.setVersion(ProgramProperties.getProgramVersion());
- options.setLicense("Copyright (C) 2016 Daniel H. Huson. This program
comes with ABSOLUTELY NO WARRANTY.");
+ options.setLicense("Copyright (C) 2017 Daniel H. Huson. This program
comes with ABSOLUTELY NO WARRANTY.");
options.comment("Mode:");
maltOptions.setMode(BlastMode.valueOfIgnoreCase(options.getOptionMandatory("m",
"mode", "Program mode", BlastMode.values(), BlastMode.BlastX.toString())));
@@ -214,7 +214,7 @@ public class MaltRun {
maltOptions.setUsePercentIdentityFilterLCA(options.getOption("mif",
"useMinPercentIdentityFilterLCA", "Use percent identity assignment filter",
maltOptions.isUsePercentIdentityFilterLCA()));
- maltOptions.setUseWeightedLCA(options.getOption("-wlca",
"weightedLCA", "Use the weighted LCA for taxonomic assignment",
Document.DEFAULT_WEIGHTED_LCA));
+ maltOptions.setUseWeightedLCA(options.getOption("-wlca",
"weightedLCA", "Use the weighted LCA for taxonomic assignment", false));
if (options.isDoHelp() || maltOptions.isUseWeightedLCA())
maltOptions.setWeightedLCAPercent(options.getOption("-wlp",
"weightedLCAPercent", "Set the percent weight to cover",
Document.DEFAULT_WEIGHTED_LCA_PERCENT));
diff --git a/src/malt/io/RMA6Writer.java b/src/malt/io/RMA6Writer.java
index 63ff3cd..6b35267 100644
--- a/src/malt/io/RMA6Writer.java
+++ b/src/malt/io/RMA6Writer.java
@@ -191,7 +191,7 @@ public class RMA6Writer {
final Document doc = new Document();
doc.setTopPercent(maltOptions.getTopPercentLCA());
- doc.setWeightedLCA(maltOptions.isUseWeightedLCA());
+ doc.setLcaAlgorithm(maltOptions.isUseWeightedLCA() ?
Document.LCAAlgorithm.weighted : Document.LCAAlgorithm.naive);
doc.setWeightedLCAPercent(maltOptions.getWeightedLCAPercent());
doc.setMinSupportPercent(maltOptions.getMinSupportPercentLCA());
doc.setMinSupport(maltOptions.getMinSupportLCA());
@@ -202,13 +202,15 @@ public class RMA6Writer {
doc.setMinPercentIdentity(maltOptions.getMinPercentIdentityLCA());
doc.setUseIdentityFilter(maltOptions.isUsePercentIdentityFilterLCA());
+ doc.setReadAssignmentMode(Document.ReadAssignmentMode.readCount);
// todo: make this an option
+
doc.getMeganFile().setFileFromExistingFile(rma6File, false);
doc.loadMeganFile();
doc.processReadHits();
// update and then save auxiliary data:
final String sampleName =
Basic.replaceFileSuffix(Basic.getFileNameWithoutPath(rma6File), "");
- SyncArchiveAndDataTable.syncRecomputedArchive2Summary(sampleName,
"LCA", doc.getBlastMode(), doc.getParameterString(), new
RMA6Connector(rma6File), doc.getDataTable(), 0);
+
SyncArchiveAndDataTable.syncRecomputedArchive2Summary(doc.getReadAssignmentMode(),
sampleName, "LCA", doc.getBlastMode(), doc.getParameterString(), new
RMA6Connector(rma6File), doc.getDataTable(), 0);
doc.saveAuxiliaryData();
} catch (CanceledException ex) {
throw new IOException(ex); // this can't happen because
ProgressPercent never throws CanceledException
diff --git a/tex/manual/manual.pdf b/tex/manual/manual.pdf
index 1241776..5915395 100644
Binary files a/tex/manual/manual.pdf and b/tex/manual/manual.pdf differ
diff --git a/tex/manual/manual.tex b/tex/manual/manual.tex
index 1c0618d..0491530 100644
--- a/tex/manual/manual.tex
+++ b/tex/manual/manual.tex
@@ -484,8 +484,8 @@ is allowed to use. This cannot be set from within the
program but rather is set
The following options are used to filter matches by significance. Matches that
do not meet all criteria specified are completely ignored.
\begin{itemize}
\setlength{\itemindent}{30pt}
-\item[\itt{--minBitScore}] Minimum bit score. Default value: 50.0.
-\item[\itt{--maxExpected}] Maximum expected score. Default value:
1.0.
+\item[\itt{--minBitScore}] Minimum bit disjointScore. Default value:
50.0.
+\item[\itt{--maxExpected}] Maximum expected disjointScore. Default
value: 1.0.
\item[{\itt{--minPercentIdentity}}] Minimum percent identity. Default value:
0.0.
\item[{\itt{--maxAlignmentsPerQuery}}] Maximum number of alignments per
query. Default value: 100.
\item[{\itt{ --maxAlignmentsPerRef}}] Maximum number of (non-overlapping)
alignments per reference. Default value: 1.
@@ -497,8 +497,8 @@ There are a number of options that are specific to the
\concept{BlastN mode}. Th
are also used in the computation of expected values.
\begin{itemize}
\setlength{\itemindent}{30pt}
-\item[\itt{--matchScore}] Use to specify the alignment match score.
Default value: 2.
-\item[\itt{--mismatchScore}] Use to specify the alignment mis-match
score. Default value: -3.
+\item[\itt{--matchScore}] Use to specify the alignment match
disjointScore. Default value: 2.
+\item[\itt{--mismatchScore}] Use to specify the alignment mis-match
disjointScore. Default value: -3.
\item[\itt{--setLambda}] Parameter Lambda \index{Lambda parameter}
for \irm{BLASTN statistics}. Default value: 0.625.
\item[\itt{--setK}] Parameter K \index{K parameter} for
BLASTN statistics. Default value: 0.41.
\end{itemize}
@@ -526,7 +526,7 @@ The program uses the LCA algorithm \cite{MEGAN2007} to
assign reads to taxa. The
\item[\itt{lca\_taxonomy}] Use to specify that the LCA algorithm should be
applied to the taxonomy classification. Similar switches are available to turn
on the use of the LCA algorithm for other classifications.
But using the LCA algorithms only makes sense when providing additional
taxonomic classifications such as the RDP tree.
\item[\itt{--topPercent}] Use to specify the \pconcept{top percent}
value for LCA algorithm. Default value is 10\%. For each read,
-only those matches are used for taxonomic placement whose bit score is within
10\% of the best score for that read.
+only those matches are used for taxonomic placement whose bit disjointScore is
within 10\% of the best disjointScore for that read.
\item[\itt{--minSupport}] Use to specify the \pconcept{min support}
value for the LCA algorithm.
\end{itemize}
@@ -586,14 +586,14 @@ OPTIONS
-mt, --maxTables [number] Set the maximum number of seed
tables to use (0=all). Default value: 0.
-rqc, --replicateQueryCache Cache results for replicated
queries. Default value: false.
Filter:
- -b, --minBitScore [number] Minimum bit score. Default value:
50.0.
- -e, --maxExpected [number] Maximum expected score. Default
value: 1.0.
+ -b, --minBitScore [number] Minimum bit disjointScore. Default
value: 50.0.
+ -e, --maxExpected [number] Maximum expected disjointScore.
Default value: 1.0.
-id, --minPercentIdentity [number] Minimum percent identity. Default
value: 0.0.
-mq, --maxAlignmentsPerQuery [number] Maximum number of alignments
per query. Default value: 25.
-mrf, --maxAlignmentsPerRef [number] Maximum number of
(non-overlapping) alignments per reference. Default value: 1.
BlastN parameters:
- -ma, --matchScore [number] Match score. Default value: 2.
- -mm, --mismatchScore [number] Mismatch score. Default value: -3.
+ -ma, --matchScore [number] Match disjointScore. Default
value: 2.
+ -mm, --mismatchScore [number] Mismatch disjointScore. Default
value: -3.
-la, --setLambda [number] Parameter Lambda for BLASTN
statistics. Default value: 0.625.
-K, --setK [number] Parameter K for BLASTN statistics.
Default value: 0.41.
BlastP and BlastX parameters:
diff --git a/tex/manual/versioninfo.tex b/tex/manual/versioninfo.tex
index c3276a4..fc03f9a 100644
--- a/tex/manual/versioninfo.tex
+++ b/tex/manual/versioninfo.tex
@@ -1 +1 @@
-\def\VERSION{{0.3.6}}
+\def\VERSION{{0.3.8}}
diff --git a/tex/manual/versioninfo_new.tex b/tex/manual/versioninfo_new.tex
index c3276a4..fc03f9a 100644
--- a/tex/manual/versioninfo_new.tex
+++ b/tex/manual/versioninfo_new.tex
@@ -1 +1 @@
-\def\VERSION{{0.3.6}}
+\def\VERSION{{0.3.8}}
diff --git a/tex/manual/versioninfo_old.tex b/tex/manual/versioninfo_old.tex
index 34ffc48..fc03f9a 100644
--- a/tex/manual/versioninfo_old.tex
+++ b/tex/manual/versioninfo_old.tex
@@ -1 +1 @@
-\def\VERSION{{0.3.5}}
+\def\VERSION{{0.3.8}}
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