From 6a8e6ec5f2cebcb8ec901add6fb64033fcd572da Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 31 May 2012 01:37:06 +0000 Subject: [PATCH] in progress --- .../application/{msa_quality.java => mcc.java} | 7 ++++--- .../archaeopteryx/tools/PhylogeneticInferrer.java | 10 ++++++++-- .../forester/archaeopteryx/tools/RunnableProcess.java | 4 ++-- .../archaeopteryx/tools/SequenceDataRetriver.java | 8 +++----- .../archaeopteryx/tools/TaxonomyDataObtainer.java | 6 +++--- forester/java/src/org/forester/util/ForesterUtil.java | 17 +++++++++++++++-- 6 files changed, 35 insertions(+), 17 deletions(-) rename forester/java/src/org/forester/application/{msa_quality.java => mcc.java} (96%) diff --git a/forester/java/src/org/forester/application/msa_quality.java b/forester/java/src/org/forester/application/mcc.java similarity index 96% rename from forester/java/src/org/forester/application/msa_quality.java rename to forester/java/src/org/forester/application/mcc.java index a350fe9..77c9a7f 100644 --- a/forester/java/src/org/forester/application/msa_quality.java +++ b/forester/java/src/org/forester/application/mcc.java @@ -36,7 +36,7 @@ import org.forester.util.CommandLineArguments; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterUtil; -public class msa_quality { +public class mcc { final static private String HELP_OPTION_1 = "help"; final static private String HELP_OPTION_2 = "h"; @@ -44,7 +44,8 @@ public class msa_quality { final static private String TO_OPTION = "t"; final static private String STEP_OPTION = "s"; final static private String WINDOW_OPTION = "w"; - final static private String PRG_NAME = "msa_quality"; + final static private String PRG_NAME = "mcc"; + final static private String PRG_DESC = "msa consensus conservation"; final static private String PRG_VERSION = "1.00"; final static private String PRG_DATE = "2012.05.18"; final static private String E_MAIL = "phylosoft@gmail.com"; @@ -89,7 +90,7 @@ public class msa_quality { } private static void printHelp() { - ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW ); + ForesterUtil.printProgramInformation( PRG_NAME, PRG_DESC, PRG_VERSION, PRG_DATE, E_MAIL, WWW ); System.out.println( "Usage:" ); System.out.println(); System.out.println( PRG_NAME + " " ); diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java index a6529a3..6cf6614 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java @@ -58,7 +58,7 @@ import org.forester.sequence.Sequence; import org.forester.tools.ConfidenceAssessor; import org.forester.util.ForesterUtil; -public class PhylogeneticInferrer implements Runnable { +public class PhylogeneticInferrer extends RunnableProcess { private Msa _msa; private final MainFrameApplication _mf; @@ -156,12 +156,14 @@ public class PhylogeneticInferrer implements Runnable { if ( ( _msa == null ) && ( _seqs == null ) ) { throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" ); } + start( _mf, "phylogenetic inference" ); if ( _msa == null ) { Msa msa = null; try { msa = inferMsa(); } catch ( final IOException e ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Could not create multiple sequence alignment with \"" + _options.getMsaPrg() + "\" and the following parameters:\n\"" @@ -175,6 +177,7 @@ public class PhylogeneticInferrer implements Runnable { return; } catch ( final Exception e ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Could not create multiple sequence alignment with \"" + _options.getMsaPrg() + "\" and the following parameters:\n\"" @@ -188,6 +191,7 @@ public class PhylogeneticInferrer implements Runnable { return; } if ( msa == null ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Could not create multiple sequence alignment with " + _options.getMsaPrg() + "\nand the following parameters:\n\"" @@ -206,6 +210,7 @@ public class PhylogeneticInferrer implements Runnable { _options.getMsaProcessingMinAllowedLength(), msa ); if ( msa == null ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Less than two sequences longer than " + _options.getMsaProcessingMinAllowedLength() @@ -237,7 +242,8 @@ public class PhylogeneticInferrer implements Runnable { ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 ); } _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" ); - _mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); + // _mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); + end( _mf ); JOptionPane.showMessageDialog( _mf, "Inference successfully completed", "Inference Completed", diff --git a/forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java b/forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java index 159ee9b..b559fba 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/RunnableProcess.java @@ -18,7 +18,7 @@ public abstract class RunnableProcess implements Runnable { } void start( final MainFrame mf, final String name ) { - mf.getMainPanel().getCurrentTreePanel().setWaitCursor(); + //mf.getMainPanel().getCurrentTreePanel().setWaitCursor(); setProcessId( mf.getProcessPool().addProcess( name ) ); mf.updateProcessMenu(); } @@ -29,7 +29,7 @@ public abstract class RunnableProcess implements Runnable { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "could not remove process " + getProcessId() + " from process pool" ); } - mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); + //mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); mf.updateProcessMenu(); } } diff --git a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java index 7aed148..4db8175 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java @@ -47,7 +47,7 @@ import org.forester.ws.uniprot.DatabaseTools; import org.forester.ws.uniprot.SequenceDatabaseEntry; import org.forester.ws.uniprot.UniProtWsTools; -public final class SequenceDataRetriver implements Runnable { +public final class SequenceDataRetriver extends RunnableProcess { private final Phylogeny _phy; private final MainFrameApplication _mf; @@ -69,13 +69,12 @@ public final class SequenceDataRetriver implements Runnable { } private void execute() { - _mf.getMainPanel().getCurrentTreePanel().setWaitCursor(); + start( _mf, "sequence data" ); SortedSet not_found = null; try { not_found = obtainSeqInformation( _phy ); } catch ( final UnknownHostException e ) { - _mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); JOptionPane.showMessageDialog( _mf, "Could not connect to \"" + getBaseUrl() + "\"", "Network error during taxonomic information gathering", @@ -83,7 +82,6 @@ public final class SequenceDataRetriver implements Runnable { return; } catch ( final IOException e ) { - _mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); e.printStackTrace(); JOptionPane.showMessageDialog( _mf, e.toString(), @@ -92,7 +90,7 @@ public final class SequenceDataRetriver implements Runnable { return; } finally { - _mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); + end( _mf ); } _treepanel.setTree( _phy ); _mf.showWhole(); diff --git a/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java b/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java index 40b02db..819466e 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/TaxonomyDataObtainer.java @@ -39,7 +39,7 @@ import org.forester.archaeopteryx.TreePanel; import org.forester.phylogeny.Phylogeny; import org.forester.ws.uniprot.UniProtWsTools; -public class TaxonomyDataObtainer implements Runnable { +public class TaxonomyDataObtainer extends RunnableProcess { private final Phylogeny _phy; private final MainFrameApplication _mf; @@ -68,7 +68,7 @@ public class TaxonomyDataObtainer implements Runnable { } private void execute() { - _mf.getMainPanel().getCurrentTreePanel().setWaitCursor(); + start( _mf, "taxonomy data" ); SortedSet not_found = null; try { not_found = AncestralTaxonomyInference.obtainDetailedTaxonomicInformation( _phy, _delete ); @@ -100,7 +100,7 @@ public class TaxonomyDataObtainer implements Runnable { return; } finally { - _mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); + end( _mf ); } _treepanel.setTree( _phy ); _mf.showWhole(); diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index 58dbf45..fcc7278 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -731,13 +731,18 @@ public final class ForesterUtil { } final public static void printProgramInformation( final String prg_name, + final String desc, final String prg_version, final String date, final String email, final String www ) { - final int l = prg_name.length() + prg_version.length() + date.length() + 4; + String my_prg_name = new String( prg_name ); + if ( !ForesterUtil.isEmpty( desc ) ) { + my_prg_name += ( " - " + desc ); + } + final int l = my_prg_name.length() + prg_version.length() + date.length() + 4; System.out.println(); - System.out.println( prg_name + " " + prg_version + " (" + date + ")" ); + System.out.println( my_prg_name + " " + prg_version + " (" + date + ")" ); for( int i = 0; i < l; ++i ) { System.out.print( "_" ); } @@ -752,6 +757,14 @@ public final class ForesterUtil { System.out.println(); } + final public static void printProgramInformation( final String prg_name, + final String prg_version, + final String date, + final String email, + final String www ) { + printProgramInformation( prg_name, null, prg_version, date, email, www ); + } + final public static void printWarningMessage( final String prg_name, final String message ) { System.out.println( "[" + prg_name + "] > warning: " + message ); } -- 1.7.10.2