JAL-3446 from applet; JAL-3374

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 2ad5bea..3de631f 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -87,6 +87,7 @@ public class SeqPanel extends JPanel
         SequenceListener, SelectionListener
 {
   /*
+   * 
    * a class that holds computed mouse position
    * - column of the alignment (0...)
    * - sequence offset (0...)
@@ -212,8 +213,6 @@ public class SeqPanel extends JPanel
 
   StringBuffer keyboardNo2;
 
-  java.net.URL linkImageURL;
-
   private final SequenceAnnotationReport seqARep;
 
   /*
@@ -244,8 +243,7 @@ public class SeqPanel extends JPanel
    */
   public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
   {
-    linkImageURL = getClass().getResource("/images/link.gif");
-    seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+    seqARep = new SequenceAnnotationReport(true);
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -293,8 +291,7 @@ public class SeqPanel extends JPanel
     int alignmentHeight = av.getAlignment().getHeight();
     if (av.getWrapAlignment())
     {
-      seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(),
-              seqCanvas.getHeight());
+      seqCanvas.calculateWrappedGeometry();
 
       /*
        * yPos modulo height of repeating width
@@ -426,8 +423,7 @@ public class SeqPanel extends JPanel
       if (editCommand != null && editCommand.getSize() > 0)
       {
         ap.alignFrame.addHistoryItem(editCommand);
-        av.firePropertyChange("alignment", null,
-                av.getAlignment().getSequences());
+        ap.av.notifyAlignment();
       }
     } finally
     {
@@ -1067,9 +1063,9 @@ public class SeqPanel extends JPanel
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
-      unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos,
-              features,
-              this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
+      unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
+              features, this.ap.getSeqPanel().seqCanvas.fr,
+              MAX_TOOLTIP_LENGTH);
 
       /*
        * add features in CDS/protein complement at the corresponding
@@ -1087,9 +1083,8 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            unshownFeatures = seqARep.appendFeaturesLengthLimit(
-                    tooltipText, pos, mf, fr2,
-                    MAX_TOOLTIP_LENGTH);
+            unshownFeatures = seqARep.appendFeatures(tooltipText,
+                    pos, mf, fr2, MAX_TOOLTIP_LENGTH);
           }
         }
       }
@@ -1245,7 +1240,7 @@ public class SeqPanel extends JPanel
   {
     char sequenceChar = sequence.getCharAt(column);
     int pos = sequence.findPosition(column);
-    setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+    setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
 
     return pos;
   }
@@ -1261,7 +1256,7 @@ public class SeqPanel extends JPanel
    * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
    * </pre>
    * 
-   * @param sequence
+   * @param seqName
    * @param seqIndex
    *          sequence position in the alignment (1..)
    * @param sequenceChar
@@ -1269,7 +1264,7 @@ public class SeqPanel extends JPanel
    * @param residuePos
    *          the sequence residue position (if not over a gap)
    */
-  protected void setStatusMessage(SequenceI sequence, int seqIndex,
+  protected void setStatusMessage(String seqName, int seqIndex,
           char sequenceChar, int residuePos)
   {
     StringBuilder text = new StringBuilder(32);
@@ -1279,7 +1274,7 @@ public class SeqPanel extends JPanel
      */
     String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
     text.append("Sequence").append(seqno).append(" ID: ")
-            .append(sequence.getName());
+            .append(seqName);
 
     String residue = null;
 
@@ -1324,7 +1319,8 @@ public class SeqPanel extends JPanel
     {
       return;
     }
-    SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+    SequenceI alignedSeq = al.getSequenceAt(sequenceIndex);
+    SequenceI ds = alignedSeq.getDatasetSequence();
     for (SearchResultMatchI m : results.getResults())
     {
       SequenceI seq = m.getSequence();
@@ -1336,8 +1332,8 @@ public class SeqPanel extends JPanel
       if (seq == ds)
       {
         int start = m.getStart();
-        setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
-                start);
+        setStatusMessage(alignedSeq.getName(), sequenceIndex,
+                seq.getCharAt(start - 1), start);
         return;
       }
     }
@@ -2902,4 +2898,45 @@ public class SeqPanel extends JPanel
   {
     return lastSearchResults;
   }
+  
+  /**
+   * scroll to the given row/column - or nearest visible location
+   * 
+   * @param row
+   * @param column
+   */
+  public void scrollTo(int row, int column)
+  {
+
+    row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+    column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+    ap.scrollTo(column, column, row, true, true);
+  }
+
+  /**
+   * scroll to the given row - or nearest visible location
+   * 
+   * @param row
+   */
+  public void scrollToRow(int row)
+  {
+
+    row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+    ap.scrollTo(ap.av.getRanges().getStartRes(),
+            ap.av.getRanges().getStartRes(), row, true, true);
+  }
+
+  /**
+   * scroll to the given column - or nearest visible location
+   * 
+   * @param column
+   */
+  public void scrollToColumn(int column)
+  {
+
+    column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+    ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true,
+            true);
+  }
+
 }