From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 17 Jan 2019 15:29:29 +0000 (+0000)
Subject: Merge branch 'develop' into Jalview-BH/JAL-3026-JAL-3063-JAXB
X-Git-Tag: Release_2_11_4_0~45^2~18^2~315
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4c132b37c867a60959dae032addd78892d996345;p=jalview.git

Merge branch 'develop' into Jalview-BH/JAL-3026-JAL-3063-JAXB

Conflicts:
	.gitignore
	resources/lang/Messages.properties
	resources/lang/Messages_es.properties
	src/jalview/commands/EditCommand.java
	src/jalview/gui/FeatureSettings.java
	src/jalview/gui/ScalePanel.java
---

4c132b37c867a60959dae032addd78892d996345
diff --cc resources/lang/Messages.properties
index fde0b1c,c248a10..9764721
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -1357,10 -1361,5 +1355,12 @@@ label.most_bound_molecules = Most Boun
  label.most_polymer_residues = Most Polymer Residues
  label.cached_structures = Cached Structures
  label.free_text_search = Free Text Search
 +label.annotation_name = Annotation Name
 +label.annotation_description = Annotation Description 
 +label.edit_annotation_name_description = Edit Annotation Name/Description
 +label.alignment = alignment
 +label.pca = PCA
 +label.create_image_of = Create {0} image of {1}
 +label.click_to_edit = Click to edit, right-click for menu
+ label.configuration = Configuration
+ label.configure_feature_tooltip = Click to configure variable colour or filters
diff --cc resources/lang/Messages_es.properties
index 8b7fd0d,232c7b4..1cca7a6
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@@ -1358,10 -1362,5 +1356,12 @@@ label.most_bound_molecules = Más Molécu
  label.most_polymer_residues = Más Residuos de Polímeros
  label.cached_structures = Estructuras en Caché
  label.free_text_search = Búsqueda de texto libre
 +label.annotation_name = Nombre de la anotación
 +label.annotation_description = Descripción de la anotación 
 +label.edit_annotation_name_description = Editar el nombre/descripción de la anotación
 +label.alignment = alineamiento
 +label.pca = ACP
 +label.create_image_of = Crear imagen {0} de {1}
 +label.click_to_edit = Haga clic para editar, clic en el botón derecho para ver el menú  
+ label.configuration = Configuración
+ label.configure_feature_tooltip = Haga clic para configurar el color o los filtros
diff --cc src/jalview/commands/EditCommand.java
index b813dcf,1a227c5..385a33e
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@@ -596,17 -607,19 +607,19 @@@ public class EditCommand implements Com
  
      for (int i = 0; i < command.seqs.length; i++)
      {
-       newDSNeeded = false;
-       newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
-       if (command.seqs[i].getLength() < 1)
+       boolean newDSNeeded = false;
+       boolean newDSWasNeeded = command.oldds != null
+               && command.oldds[i] != null;
+       SequenceI sequence = command.seqs[i];
+       if (sequence.getLength() < 1)
        {
-         // ie this sequence was deleted, we need to
-         // readd it to the alignment
+         /*
+          * sequence was deleted; re-add it to the alignment
+          */
          if (command.alIndex[i] < command.al.getHeight())
          {
 -          List<SequenceI> sequences;
 -          synchronized (sequences = command.al.getSequences())
 +          List<SequenceI> sequences = command.al.getSequences();
 +          synchronized (sequences)
            {
              if (!(command.alIndex[i] < 0))
              {
@@@ -1315,29 -1443,45 +1443,45 @@@
  
    public class Edit
    {
-     public SequenceI[] oldds;
 -    private SequenceI[] oldds;
++    SequenceI[] oldds;
+ 
+     /**
+      * start and end of sequence prior to edit
+      */
 -    private Range[] oldStartEnd;
++    Range[] oldStartEnd;
  
 -    private boolean fullAlignmentHeight = false;
 +    boolean fullAlignmentHeight = false;
  
-     Hashtable<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
 -    private Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
++    Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
+ 
 -    private Map<String, Annotation[]> deletedAnnotations;
++    Map<String, Annotation[]> deletedAnnotations;
  
-     Hashtable<String, Annotation[]> deletedAnnotations;
+     /*
+      * features deleted by the cut (re-add on Undo)
+      * (including the original of any shortened features)
+      */
 -    private Map<SequenceI, List<SequenceFeature>> deletedFeatures;
++    Map<SequenceI, List<SequenceFeature>> deletedFeatures;
  
-     Hashtable<SequenceI, List<SequenceFeature>> editedFeatures;
+     /*
+      * shortened features added by the cut (delete on Undo)
+      */
 -    private Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
++    Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
  
 -    private AlignmentI al;
 +    AlignmentI al;
  
-     Action command;
 -    final private Action command;
++    final Action command;
  
      char[][] string;
  
      SequenceI[] seqs;
  
 -    private int[] alIndex;
 +    int[] alIndex;
  
-     int position, number;
 -    private int position;
++    int position;
+ 
 -    private int number;
++    int number;
  
 -    private char gapChar;
 +    char gapChar;
  
      public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
              char gap)
diff --cc src/jalview/gui/ScalePanel.java
index 5da14b3,6abee08..f617d0f
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@@ -276,11 -275,12 +276,14 @@@ public class ScalePanel extends JPane
    public void mouseReleased(MouseEvent evt)
    {
      mouseDragging = false;
 +    ap.getSeqPanel().stopScrolling();
  
 +    // todo res calculation should be a method on AlignViewport
-     int res = (evt.getX() / av.getCharWidth())
+     int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+ 
+     int res = (xCords / av.getCharWidth())
              + av.getRanges().getStartRes();
+ 
      if (av.hasHiddenColumns())
      {
        res = av.getAlignment().getHiddenColumns()