Merge pull request #300 from kpepper/perf_fixes

Various fixes

README.md

@@ -14,7 +14,7 @@ The Artemis Software is a set of software tools for genome browsing and annotati
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtq010-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btq010)   
 [![status](https://img.shields.io/badge/Bioinformatics-10.1093%2Fbioinformatics%2Fbtn578-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/btn578)  
 
-![GitHub Releases (by Release)](https://img.shields.io/github/downloads/sanger-pathogens/artemis/v18.0.2/total)
+![GitHub Releases (by Release)](https://img.shields.io/github/downloads/sanger-pathogens/artemis/v18.1.0/total)
 
 ## Contents
   * [Introduction](#introduction)

etc/feature_keys_gff

@@ -78,4 +78,5 @@ repeat_unit     	ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontolo
 #stem_loop       	ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified allele citation evidence function gene label locus_tag map note comment operon partial standard_name 
 #terminator      	ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified allele citation evidence gene label locus_tag map note comment operon partial standard_name 
 #transit_peptide 	ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified allele citation codon codon_start evidence function gene label locus_tag map note comment partial product pseudo standard_name
-
+low_complexity_region	ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified note comment private score
+tandem_repeat 			ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified score

etc/key_mapping

@@ -27,3 +27,5 @@ nucleotide_match                           misc_feature    note=nucleotide_match
 uORF                                       misc_feature    note=uORF
 sORF                                       misc_feature    note=sORF
 tnaORF                                     misc_feature    note=tnaORF
+low_complexity_region                      misc_feature    note=low_complexity_region
+tandem_repeat                              repeat_region   rpt_type=tandem

etc/log4j.properties

@@ -41,10 +41,12 @@ log4j.logger.uk.ac.sanger.artemis.components.alignment.LookSeqPanel=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.components.alignment.BamView=INFO, R
 log4j.logger.uk.ac.sanger.artemis.components.variant=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.io.ReadAndWriteEntry=DEBUG, R
-log4j.logger.uk.ac.sanger.artemis.io.GFFStreamFeature=DEBUG, R
+log4j.logger.uk.ac.sanger.artemis.io.GFFStreamFeature=INFO, R
+log4j.logger.uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry=INFO, R
 log4j.logger.uk.ac.sanger.artemis.util.FTPSeekableStream=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.plot.UserDataAlgorithm=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.ComparisonDataFactory=INFO, R
+log4j.logger.uk.ac.sanger.artemis.components.genebuilder.GeneUtils=ERROR, R
 
 #log4j.logger.com.ibatis.common.jdbc.SimpleDataSource=DEBUG, stdout, R
 #log4j.logger.com.ibatis.common.jdbc.ScriptRunner=DEBUG, stdout, R
@@ -56,7 +58,6 @@ log4j.logger.java.sql.ResultSet=INFO, R
 
 # j2ssh
 log4j.logger.com.sshtools.j2ssh=WARN, R
-# Pattern to output the caller's file name and line number.
 
 !-----------------------------------------------------------------------------!
 ! Configure appenders (log destinations/targets) and their options            !
@@ -65,13 +66,13 @@ log4j.logger.com.sshtools.j2ssh=WARN, R
 log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
 log4j.appender.stdout.layout.ConversionPattern=%5p [%t] (%F:%L) - %m%n
-#log4j.appender.stdout.layout.ConversionPattern=%m%n
 log4j.appender.Default=uk.ac.sanger.artemis.components.LogViewer
 log4j.appender.R=uk.ac.sanger.artemis.components.LogViewer
-log4j.appender.R.MaxLogLines=2000
 log4j.appender.R.layout=org.apache.log4j.PatternLayout
-#log4j.appender.R.layout.ConversionPattern=%5p [%t] %c - %m%n
 log4j.appender.R.layout.ConversionPattern=%d{dd MMM HH:mm:ss} - %m%n
+# The next property determines the number of lines we see in the log viewer screen.
+# If it's too big then we will get display performance impacts
+log4j.appender.R.MaxLogLines=300
 
 !-------------------------RollingFileAppender OPTIONS-------------------------!
 log4j.appender.LOGFILE=org.apache.log4j.DailyRollingFileAppender
@@ -81,11 +82,3 @@ log4j.appender.LOGFILE.DatePattern='.'yyyy-MM-dd
 #log4j.appender.LOGFILE.Threshold=INFO
 log4j.appender.LOGFILE.layout=org.apache.log4j.PatternLayout
 log4j.appender.LOGFILE.layout.ConversionPattern=%d{dd MMM yyyy HH:mm:ss,SSS} %-4r [%t] %-5p %c %x - %m%n
-
-
-#log4j.appender.srv=org.apache.log4j.net.SocketAppender
-#log4j.appender.srv.layout=org.apache.log4j.PatternLayout
-#log4j.appender.srv.RemoteHost=localhost
-#log4j.appender.srv.Port=10105
-#log4j.appender.srv.LocationInfo=false
-#log4j.appender.srv.layout.ConversionPattern=%d{dd MMM yyyy HH:mm:ss,SSS} %X{username} %X{host} %-4r [%t] %-5p %c %x - %m%n

etc/options

@@ -2,8 +2,6 @@
 
 # (Note that comment lines start with a hash (#) symbol)
 
-# $Header: //tmp/pathsoft/artemis/etc/options,v 1.73 2009-08-06 16:15:19 tjc Exp $
-
 # This file should contain option settings that look like this:
 #
 # option_name = option_value
@@ -305,11 +303,11 @@ colour_of_GFF = 11
 colour_of_start_codon = 6
 
 # suffixes used on files that contain features - used in file requesters
-feature_file_suffixes = tab embl gbk genbank tab_embl gff feature feat \
+feature_file_suffixes = tab embl gbk genbank tab_embl gff gff3 feature feat \
    art artemis
 
 # suffixes used on files that contain sequence - used in file requesters
-sequence_file_suffixes = embl gbk genbank gff tab_embl seq dna \
+sequence_file_suffixes = embl gbk genbank gff gff3 tab_embl seq dna dat \
    art artemis fa fasta fas gb fna ffn
 
 # the default height for the base plot window

etc/versions

@@ -1,4 +1,4 @@
-Artemis Release 18.0.3
-ACT Release 18.0.3
-DNAPlotter Release 18.0.3
-BamView 18.0.3
+Artemis Release 18.1.0
+ACT Release 18.1.0
+DNAPlotter Release 18.1.0
+BamView 18.1.0

etc/writedb_entry

@@ -12,6 +12,7 @@
 
 QUIET=no
 PROXY_SETTINGS=
+HELP_FLAG=false
 
 add_proxy_properties() {
 
@@ -80,6 +81,10 @@ while test $# != 0
        DEFAULT_CONNECTION="$1" ;;
     -D*)
        FLAGS="$FLAGS $1" ;;
+    -help)
+       HELP_FLAG=true ;;
+    -h)
+       HELP_FLAG=true ;;
     *) break ;;
     esac
     shift
@@ -109,7 +114,7 @@ do
 done
 
 # Check that a database connection has been provided
-if [[ "$DEFAULT_CONNECTION" = "" ]]
+if [[ "$DEFAULT_CONNECTION" = "" ]] && [[ "$HELP_FLAG" != "true" ]]
 then 
 	echo "ERROR: Please supply a database connection argument"
 	exit 1

pom.xml

@@ -5,7 +5,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>uk.ac.sanger</groupId>
 	<artifactId>artemis</artifactId>
-	<version>18.0.3</version>
+	<version>18.1.0</version>
 
 	<name>Artemis</name>
 	<description>Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

src/main/java/uk/ac/sanger/artemis/Entry.java

@@ -228,7 +228,8 @@ public void save(final File file, final int destination_type,
     final EntryInformation artemis_entry_information;
 
     if((getEMBLEntry() instanceof DatabaseDocumentEntry ||
-        getEMBLEntry() instanceof GFFDocumentEntry) &&
+        getEMBLEntry() instanceof GFFDocumentEntry || 
+        getEMBLEntry() instanceof IndexedGFFDocumentEntry) &&
        destination_type == DocumentEntryFactory.EMBL_FORMAT)
       artemis_entry_information = Options.getArtemisEntryInformation();
     else
@@ -1164,6 +1165,11 @@ private void fireAction(Vector<ChangeListener> listeners, ChangeEvent event)
   private Feature
     getFeatureOf(uk.ac.sanger.artemis.io.Feature embl_feature) 
   {
+	if (embl_feature == null)
+	{
+	  return null;
+	}
+
     final Feature test_feature =(Feature) embl_feature.getUserData();
 
     if(test_feature == null) 

src/main/java/uk/ac/sanger/artemis/FeatureSegment.java

@@ -189,7 +189,7 @@ public Marker getEnd () {
    **/
   void setStartPosition (final int position)
       throws OutOfRangeException {
-    getStart ().setPosition (position);
+    start.setPosition (position);
     updateRange ();
   }
 
@@ -198,7 +198,7 @@ void setStartPosition (final int position)
    **/
   void setEndPosition (final int position)
       throws OutOfRangeException {
-    getEnd ().setPosition (position);
+    end.setPosition (position);
     updateRange ();
   }
 
@@ -216,8 +216,8 @@ public Range getRawRange () {
   public MarkerRange getMarkerRange () {
     try {
       return new MarkerRange (getFeature ().getStrand (),
-                              getStart ().getPosition (),
-                              getEnd ().getPosition ());
+                              start.getPosition (),
+                              end.getPosition ());
     } catch (OutOfRangeException e) {
       throw new Error ("internal error - " + e);
     }
@@ -236,7 +236,7 @@ public void removeFromFeature ()
    *  Return the number of bases in this feature (total of all segments).
    **/
   public int getBaseCount () {
-    return getEnd ().getPosition () - getStart ().getPosition () + 1;
+    return end.getPosition () - start.getPosition () + 1;
   }
 
   /**
@@ -245,8 +245,8 @@ public int getBaseCount () {
   public String getBases () {
     final Strand strand = getFeature ().getStrand ();
     try {
-      return strand.getSubSequence (new Range (getStart ().getPosition (),
-                                               getEnd ().getPosition ()));
+      return strand.getSubSequence (new Range (start.getPosition (),
+                                               end.getPosition ()));
     } catch (OutOfRangeException e) {
       throw new Error ("internal error - unexpected exception: " + e);
     }
@@ -306,11 +306,11 @@ private void updateRange () {
 
     try {
       if (getFeature ().isForwardFeature ()) {
-        new_range = range.change (getStart ().getRawPosition (),
-                                  getEnd ().getRawPosition ());
+        new_range = range.change (start.getRawPosition (),
+                                  end.getRawPosition ());
       } else {
-        new_range = range.change (getEnd ().getRawPosition (),
-                                  getStart ().getRawPosition ());
+        new_range = range.change (end.getRawPosition (),
+                                  start.getRawPosition ());
       }
 
       range = new_range;
@@ -440,7 +440,7 @@ else if(this_direction != direction)
   public int getFrameID () {
     // this will be 0, 1 or 2 depending on which frame the segment is in
     final int start_base_modulo =
-      (getStart ().getPosition () - 1 + getFrameShift ()) % 3;
+      (start.getPosition () - 1 + getFrameShift ()) % 3;
 
 //  if (getFeature ().getStrand ().isForwardStrand ()) 
     if(isForwardSegment())

src/main/java/uk/ac/sanger/artemis/Selection.java

@@ -239,7 +239,8 @@ public void add (final FeatureVector features) {
    *    selection.
    **/
   private boolean addWithoutEvent (final Feature feature) {
-    if (features.contains (feature)) {
+
+    if (feature != null && features.contains (feature)) {
       return false;
       // do nothing
     } else {

src/main/java/uk/ac/sanger/artemis/SimpleEntryGroup.java

@@ -490,8 +490,16 @@ public FeatureVector getFeaturesInIndexRange(final int start_index,
   {
     final FeatureVector return_vector = new FeatureVector();
 
+    Feature f = null;
+
     for(int i = start_index; i <= end_index; ++i) 
-      return_vector.add(featureAt(i));
+    {
+      f = featureAt(i);
+      if (f != null) 
+      {
+    	  return_vector.add(featureAt(i));
+      }
+    }
 
     return return_vector;
   }

src/main/java/uk/ac/sanger/artemis/components/EntryFileDialog.java

@@ -31,6 +31,7 @@
 import uk.ac.sanger.artemis.io.Entry;
 import uk.ac.sanger.artemis.io.DocumentEntryFactory;
 import uk.ac.sanger.artemis.io.GFFDocumentEntry;
+import uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry;
 import uk.ac.sanger.artemis.io.ReadFormatException;
 import uk.ac.sanger.artemis.io.EntryInformation;
 import uk.ac.sanger.artemis.io.EntryInformationException;
@@ -470,7 +471,8 @@ else if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry ||
         {
           DocumentEntryFactory.REMOVE_PRODUCT_FROM_PSEUDOGENE = removeProductForPseudo.isSelected();
           if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry ||
-             entry.getEMBLEntry() instanceof GFFDocumentEntry)
+             entry.getEMBLEntry() instanceof GFFDocumentEntry ||
+             entry.getEMBLEntry() instanceof IndexedGFFDocumentEntry)
             ReadAndWriteEntry.writeDatabaseEntryToFile(entry, file, 
                 flattenGeneModel.isSelected(), 
                 ignoreObsoleteFeatures.isSelected(), false, 

src/main/java/uk/ac/sanger/artemis/components/FeatureList.java

@@ -450,7 +450,7 @@ private void handleCanvasMousePress(final MouseEvent event)
       final Feature clicked_feature =
         getEntryGroup().featureAt(clicked_feature_index);
 
-      if(selected_features.contains(clicked_feature)) 
+      if(clicked_feature != null && selected_features.contains(clicked_feature)) 
       {
         getSelection().remove(clicked_feature);
         getSelection().removeSegmentsOf(clicked_feature);
@@ -527,7 +527,7 @@ private void onSelectionChange()
           ++i)
       {
         final Feature this_feature = entry_group.featureAt(i);
-        if(selected_features.contains(this_feature))
+        if(this_feature != null && selected_features.contains(this_feature))
         {
           a_selected_feature_is_visible = true;
           break;
@@ -603,6 +603,7 @@ protected void paintComponent(Graphics g)
       {
         final Feature this_feature  = features_in_view.elementAt(i);
         final String feature_string = makeFeatureString(this_feature, false);
+
         drawFeatureLine(g, this_feature, feature_string);
       }
     }

src/main/java/uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java

@@ -1,7 +1,7 @@
 /* GeneUtils.java
  *
  * This file is part of Artemis
- * Copyright (C) 2007  Genome Research Limited
+ * Copyright (C) 2019  Genome Research Limited
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -43,6 +43,7 @@
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 
+import org.apache.log4j.Logger;
 import org.gmod.schema.general.DbXRef;
 import org.gmod.schema.sequence.FeatureCvTerm;
 import org.gmod.schema.sequence.FeatureDbXRef;
@@ -99,6 +100,9 @@ public class GeneUtils
   private static StringVector featuresToUpdateResidues = 
     Options.getOptions().getOptionValues("sequence_update_features");
 
+  /** Logging instance. */
+  private static Logger logger = Logger.getLogger(GeneUtils.class);
+
   static
   {
     hideFeatures.add("polypeptide");
@@ -1453,6 +1457,16 @@ public static String getUniqueName(final Feature feature)
     {
       e.printStackTrace();
     }
+    catch(NullPointerException e)
+    {
+      StringBuilder buf = new StringBuilder(80);
+      buf.append("Feature at position ")
+         .append(feature.getFirstBase())
+         .append("-")
+         .append(feature.getLastBase())
+         .append(" has no ID");
+      logger.warn(buf.toString());
+    }
     return null;
   }