sequences are private in SequenceGroup

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 3e38254..2451a96 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -113,8 +113,7 @@ public class AlignmentPanel extends GAlignmentPanel
         switch (evt.getKeyCode())\r
         {\r
           case 27: // escape key\r
-            av.setSelectionGroup(null);\r
-            repaint();\r
+            alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);\r
 \r
             break;\r
 \r
@@ -698,8 +697,14 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
     if (av.getWrapAlignment())\r
     {\r
-      int max = av.alignment.getWidth() /\r
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;\r
+      int maxwidth = av.alignment.getWidth();\r
+\r
+      if (av.hasHiddenColumns)\r
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+      int max = maxwidth /\r
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +\r
+          1;\r
 \r
 \r
       vscroll.setMaximum(max);\r
@@ -839,7 +844,7 @@ public class AlignmentPanel extends GAlignmentPanel
     for (int i = startSeq; i < endSeq; i++)\r
     {\r
       if ( (av.getSelectionGroup() != null) &&\r
-          av.getSelectionGroup().sequences.contains(\r
+          av.getSelectionGroup().getSequences(false).contains(\r
               av.getAlignment().getSequenceAt(i)))\r
       {\r
         currentColor = Color.gray;\r
@@ -918,10 +923,15 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
     int idWidth = calculateIdWidth().width + 4;\r
 \r
+    int maxwidth = av.alignment.getWidth();\r
+    if (av.hasHiddenColumns)\r
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+\r
     int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
         idWidth);\r
 \r
-    int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);\r
+    int totalHeight = cHeight * (maxwidth / resWidth + 1);\r
 \r
     pg.setColor(Color.white);\r
     pg.fillRect(0, 0, pwidth, pheight);\r
@@ -986,8 +996,12 @@ public class AlignmentPanel extends GAlignmentPanel
 \r
   void makeAlignmentImage(int type, File file)\r
   {\r
+    int maxwidth = av.alignment.getWidth();\r
+    if (av.hasHiddenColumns)\r
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);\r
+\r
     int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
-    int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
+    int width = idPanel.getWidth() + (maxwidth * av.charWidth);\r
     if (idPanel.getWidth() == 0)\r
     {\r
       width += calculateIdWidth().getWidth() + 4;\r
@@ -1002,7 +1016,6 @@ public class AlignmentPanel extends GAlignmentPanel
         width = alignFrame.getWidth() - 22;\r
       }\r
       else\r
-\r
         width = seqPanel.getWidth() + idPanel.getWidth();\r
 \r
     }\r
@@ -1235,7 +1248,12 @@ public class AlignmentPanel extends GAlignmentPanel
         + hgap\r
         + annotationHeight;\r
 \r
-    int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
+    int maxwidth = av.alignment.getWidth();\r
+    if (av.hasHiddenColumns)\r
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+\r
+    int height = ( (maxwidth / chunkWidth) + 1) * cHeight;\r
 \r
     return height;\r
   }\r