X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=deabf46f31c3a24036a1fddcdfdd903658dc1936;hb=792f60087e6b756c77618dee886d00c52587b641;hp=8c29ca5a6c1d093c59297d83e81435b96cbdc14d;hpb=3f91bb1385ab9ac8fdd15e3bc9378f5b554e1642;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 8c29ca5..deabf46 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -27,6 +27,8 @@ import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
@@ -39,6 +41,26 @@ import java.util.Map;
  */
 public class SequenceGroup implements AnnotatedCollectionI
 {
+  // TODO ideally this event notification functionality should be separated into
+  // a
+  // subclass of ViewportProperties similarly to ViewportRanges. Done here as
+  // quick fix for JAL-2665
+  public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
+
+  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
+  public void addPropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.addPropertyChangeListener(listener);
+  }
+
+  public void removePropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.removePropertyChangeListener(listener);
+  }
+  // end of event notification functionality initialisation
+
   String groupName;
 
   String description;
@@ -79,11 +101,15 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public ResidueShaderI cs;
 
-  // start column (base 0)
-  int startRes = 0;
+  /**
+   * start column (base 0)
+   */
+  private int startRes = 0;
 
-  // end column (base 0)
-  int endRes = 0;
+  /**
+   *  end column (base 0)
+   */
+  private int endRes = 0;
 
   public Color outlineColour = Color.black;
 
@@ -110,13 +136,23 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private boolean normaliseSequenceLogo;
 
-  /**
-   * @return the includeAllConsSymbols
+  /*
+   * visibility of rows or represented rows covered by group
    */
-  public boolean isShowSequenceLogo()
-  {
-    return showSequenceLogo;
-  }
+  private boolean hidereps = false;
+
+  /*
+   * visibility of columns intersecting this group
+   */
+  private boolean hidecols = false;
+
+  AlignmentAnnotation consensus = null;
+
+  AlignmentAnnotation conservation = null;
+
+  private boolean showConsensusHistogram;
+
+  private AnnotatedCollectionI context;
 
   /**
    * Creates a new SequenceGroup object.
@@ -176,15 +212,20 @@ public class SequenceGroup implements AnnotatedCollectionI
       displayBoxes = seqsel.displayBoxes;
       displayText = seqsel.displayText;
       colourText = seqsel.colourText;
+      
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
-      cs = seqsel.cs;
+      cs = new ResidueShader((ResidueShader) seqsel.cs);
       if (seqsel.description != null)
       {
         description = new String(seqsel.description);
       }
       hidecols = seqsel.hidecols;
       hidereps = seqsel.hidereps;
+      showNonconserved = seqsel.showNonconserved;
+      showSequenceLogo = seqsel.showSequenceLogo;
+      normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
+      showConsensusHistogram = seqsel.showConsensusHistogram;
       idColour = seqsel.idColour;
       outlineColour = seqsel.outlineColour;
       seqrep = seqsel.seqrep;
@@ -201,6 +242,11 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
+  public boolean isShowSequenceLogo()
+  {
+    return showSequenceLogo;
+  }
+
   public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
   {
     int iSize = sequences.size();
@@ -477,6 +523,8 @@ public class SequenceGroup implements AnnotatedCollectionI
       if (s != null && !sequences.contains(s))
       {
         sequences.add(s);
+        changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+                sequences.size() - 1, sequences.size());
       }
 
       if (recalc)
@@ -601,8 +649,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     conservation.description = "Conservation for group " + getName()
             + " less than " + consPercGaps + "% gaps";
     // preserve width if already set
-    int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
-            : endRes + 1)
+    int aWidth = (conservation.annotations != null)
+            ? (endRes < conservation.annotations.length
+                    ? conservation.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     conservation.annotations = null;
     conservation.annotations = new Annotation[aWidth]; // should be alignment
@@ -622,8 +672,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     consensus.description = "Percent Identity";
     consensusData = cnsns;
     // preserve width if already set
-    int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
-            : endRes + 1)
+    int aWidth = (consensus.annotations != null)
+            ? (endRes < consensus.annotations.length
+                    ? consensus.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     consensus.annotations = null;
     consensus.annotations = new Annotation[aWidth]; // should be alignment width
@@ -670,6 +722,8 @@ public class SequenceGroup implements AnnotatedCollectionI
     synchronized (sequences)
     {
       sequences.remove(s);
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+              sequences.size() + 1, sequences.size());
 
       if (recalc)
       {
@@ -702,11 +756,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Set the first column selected by this group. Runs from 0<=i<N_cols
    * 
-   * @param i
+   * @param newStart
    */
-  public void setStartRes(int i)
+  public void setStartRes(int newStart)
   {
-    startRes = i;
+    int before = startRes;
+   startRes= Math.max(0,newStart); // sanity check for negative start column positions
+   changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+    
+
+
   }
 
   /**
@@ -716,7 +775,9 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void setEndRes(int i)
   {
+    int before = endRes;
     endRes = i;
+    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
   }
 
   /**
@@ -957,11 +1018,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of rows or represented rows covered by group
-   */
-  private boolean hidereps = false;
-
-  /**
    * set visibility of sequences covered by (if no sequence representative is
    * defined) or represented by this group.
    * 
@@ -983,11 +1039,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of columns intersecting this group
-   */
-  private boolean hidecols = false;
-
-  /**
    * set intended visibility of columns covered by this group
    * 
    * @param visibility
@@ -1049,13 +1100,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.showNonconserved = displayNonconserved;
   }
 
-  AlignmentAnnotation consensus = null, conservation = null;
-
-  /**
-   * flag indicating if consensus histogram should be rendered
-   */
-  private boolean showConsensusHistogram;
-
   /**
    * set this alignmentAnnotation object as the one used to render consensus
    * annotation
@@ -1302,11 +1346,12 @@ public class SequenceGroup implements AnnotatedCollectionI
     ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
-      if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
-              .equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
-              && (label == null || (ann.label != null && ann.label
-                      .equals(label))))
+      if ((calcId == null || (ann.getCalcId() != null
+              && ann.getCalcId().equals(calcId)))
+              && (seq == null || (ann.sequenceRef != null
+                      && ann.sequenceRef == seq))
+              && (label == null
+                      || (ann.label != null && ann.label.equals(label))))
       {
         aa.add(ann);
       }
@@ -1342,12 +1387,13 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
+      int before = sequences.size();
       sequences.clear();
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
+              sequences.size());
     }
   }
 
-  private AnnotatedCollectionI context;
-
   /**
    * Sets the alignment or group context for this group, and whether it is
    * defined as a group
@@ -1432,7 +1478,8 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public boolean isNucleotide()
   {
-    if (context != null) {
+    if (context != null)
+    {
       return context.isNucleotide();
     }
     return false;