X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=c8a2ec90ef9b6646fd22d77ec69ccb030ed0d602;hb=5f4f772b4ce40f2ea987cb03dd2c06ec1f48ba67;hp=4e789b9f580c05ae3c079faea99552da0c195547;hpb=461d9cd18036c268ae890fcf2418e9ac181b3c61;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 4e789b9..c8a2ec9 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -44,7 +44,7 @@ import javax.swing.Timer;
 import javax.swing.ToolTipManager;
 
 import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -243,6 +243,7 @@ public class SeqPanel extends JPanel
    */
   public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
   {
+    setName("SeqPanel");
     seqARep = new SequenceAnnotationReport(true);
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
@@ -276,6 +277,9 @@ public class SeqPanel extends JPanel
   /**
    * Computes the column and sequence row (and possibly annotation row when in
    * wrapped mode) for the given mouse position
+   * <p>
+   * Mouse position is not set if in wrapped mode with the cursor either between
+   * sequences, or over the left or right vertical scale.
    * 
    * @param evt
    * @return
@@ -342,6 +346,9 @@ public class SeqPanel extends JPanel
   /**
    * Returns the aligned sequence position (base 0) at the mouse position, or
    * the closest visible one
+   * <p>
+   * Returns -1 if in wrapped mode with the mouse over either left or right
+   * vertical scale.
    * 
    * @param evt
    * @return
@@ -423,8 +430,7 @@ 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
     {
@@ -477,47 +483,80 @@ public class SeqPanel extends JPanel
 
   void moveCursor(int dx, int dy)
   {
-    seqCanvas.cursorX += dx;
-    seqCanvas.cursorY += dy;
-
+    moveCursor(dx, dy,false);
+  }
+  void moveCursor(int dx, int dy, boolean nextWord)
+  {
     HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
-    if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
+    if (nextWord)
     {
-      int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
-
-      if (!hidden.isVisible(seqCanvas.cursorX))
-      {
-        int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
-        int[] region = hidden.getRegionWithEdgeAtRes(visx);
-
-        if (region != null) // just in case
+      int maxHeight=av.getAlignment().getHeight();
+      SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+      // look for next gap or residue
+      boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
+      int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR;
+      do
+      {
+        lastP = p;
+        lastR = r;
+        if (dy != 0)
         {
-          if (dx == 1)
+          r += dy;
+          if (r < 0)
           {
-            // moving right
-            seqCanvas.cursorX = region[1] + 1;
+            r = 0;
           }
-          else if (dx == -1)
+          if (r >= maxHeight)
           {
-            // moving left
-            seqCanvas.cursorX = region[0] - 1;
+            r = maxHeight - 1;
           }
+          seqAtRow = av.getAlignment().getSequenceAt(r);
         }
-        seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
-      }
+        p = nextVisible(hidden, maxWidth, p, dx);
+      } while ((dx != 0 ? p != lastP : r != lastR)
+              && isGap == Comparison.isGap(seqAtRow.getCharAt(p)));
+      seqCanvas.cursorX=p;
+      seqCanvas.cursorY=r;
+    } else {
+      int maxWidth = av.getAlignment().getWidth();
+      seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx);
+      seqCanvas.cursorY += dy;
+    }
+    scrollToVisible(false);
+  }
 
-      if (seqCanvas.cursorX >= maxWidth
-              || !hidden.isVisible(seqCanvas.cursorX))
+  private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx)
+  {
+    int newCursorX=original+dx;
+    if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX))
+    {
+      int visx = hidden.absoluteToVisibleColumn(newCursorX - dx);
+      int[] region = hidden.getRegionWithEdgeAtRes(visx);
+
+      if (region != null) // just in case
       {
-        seqCanvas.cursorX = original;
+        if (dx == 1)
+        {
+          // moving right
+          newCursorX = region[1] + 1;
+        }
+        else if (dx == -1)
+        {
+          // moving left
+          newCursorX = region[0] - 1;
+        }
       }
     }
-
-    scrollToVisible(false);
+    newCursorX = (newCursorX < 0) ? 0 : newCursorX;
+    if (newCursorX >= maxWidth
+            || !hidden.isVisible(newCursorX))
+    {
+      newCursorX = original;
+    }
+    return newCursorX;
   }
-
   /**
    * Scroll to make the cursor visible in the viewport.
    * 
@@ -909,11 +948,12 @@ public class SeqPanel extends JPanel
     AlignFrame af = Desktop.getAlignFrameFor(complement);
     FeatureRendererModel fr2 = af.getFeatureRenderer();
 
-    int j = results.getSize();
+    List<SearchResultMatchI> matches = results.getResults();
+    int j = matches.size();
     List<String> infos = new ArrayList<>();
     for (int i = 0; i < j; i++)
     {
-      SearchResultMatchI match = results.getResults().get(i);
+      SearchResultMatchI match = matches.get(i);
       int pos = match.getStart();
       if (pos == match.getEnd())
       {
@@ -1084,7 +1124,7 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            unshownFeatures = seqARep.appendFeatures(tooltipText,
+            unshownFeatures += seqARep.appendFeatures(tooltipText,
                     pos, mf, fr2, MAX_TOOLTIP_LENGTH);
           }
         }
@@ -1141,7 +1181,8 @@ public class SeqPanel extends JPanel
 
     String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
             anns);
-    if (!tooltip.equals(lastTooltip))
+    boolean tooltipChanged = tooltip == null ? lastTooltip != null : !tooltip.equals(lastTooltip);
+    if (tooltipChanged)
     {
       lastTooltip = tooltip;
       lastFormattedTooltip = tooltip == null ? null
@@ -2762,7 +2803,7 @@ public class SeqPanel extends JPanel
     {
       if (av.getAlignment() == null)
       {
-        Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+        Console.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
                 + " ViewId=" + av.getViewId()
                 + " 's alignment is NULL! returning immediately.");
         return;
@@ -2939,5 +2980,4 @@ public class SeqPanel extends JPanel
     ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true,
             true);
   }
-
 }