validCharWidth moved to viewport

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 44330fa..d4ba5ea 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,8 +61,9 @@ public class AlignViewport
     SequenceGroup selectionGroup;\r
     int charHeight;\r
     int charWidth;\r
+    boolean validCharWidth;\r
     int wrappedWidth;\r
-    Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+    Font font;\r
     AlignmentI alignment;\r
     ColumnSelection colSel = new ColumnSelection();\r
     int threshold;\r
@@ -71,12 +72,22 @@ public class AlignViewport
     boolean scaleAboveWrapped = false;\r
     boolean scaleLeftWrapped = true;\r
     boolean scaleRightWrapped = true;\r
+    boolean hasHiddenColumns = false;\r
+    boolean hasHiddenRows = false;\r
+\r
+    boolean cursorMode = false;\r
+\r
+    // The following vector holds the features which are\r
+    // currently visible, in the correct order or rendering\r
+    Hashtable featuresDisplayed = null;\r
+\r
 \r
     /** DOCUMENT ME!! */\r
     public Vector vconsensus;\r
     AlignmentAnnotation consensus;\r
     AlignmentAnnotation conservation;\r
     AlignmentAnnotation quality;\r
+    boolean autoCalculateConsensus = true;\r
 \r
     /** DOCUMENT ME!! */\r
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
@@ -88,6 +99,10 @@ public class AlignViewport
 \r
     boolean isDataset = false;\r
 \r
+    boolean antiAlias = false;\r
+\r
+    boolean padGaps = false;\r
+\r
 \r
     public AlignViewport(AlignmentI al, boolean dataset)\r
     {\r
@@ -113,6 +128,8 @@ public class AlignViewport
         this.startSeq = 0;\r
         this.endSeq = alignment.getHeight() - 1;\r
 \r
+      antiAlias = Cache.getDefault("ANTI_ALIAS", false);\r
+\r
       showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);\r
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
       showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
@@ -120,6 +137,10 @@ public class AlignViewport
       showQuality = Cache.getDefault("SHOW_QUALITY", true);\r
       showIdentity = Cache.getDefault("SHOW_IDENTITY", true);\r
 \r
+      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);\r
+\r
+      padGaps = Cache.getDefault("PAD_GAPS", false);\r
+\r
        String fontName = Cache.getDefault("FONT_NAME", "SansSerif");\r
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;\r
        String fontSize = Cache.getDefault("FONT_SIZE", "10");\r
@@ -174,11 +195,16 @@ public class AlignViewport
      *\r
      * @param b DOCUMENT ME!\r
      */\r
-    public void showSequenceFeatures(boolean b)\r
+    public void setShowSequenceFeatures(boolean b)\r
     {\r
         showSequenceFeatures = b;\r
     }\r
 \r
+    public boolean getShowSequenceFeatures()\r
+    {\r
+      return showSequenceFeatures;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      */\r
@@ -292,12 +318,19 @@ public class AlignViewport
       }\r
       catch (OutOfMemoryError error)\r
       {\r
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-            "Out of memory calculating conservation!!"\r
-            +\r
-            "\nSee help files for increasing Java Virtual Machine memory."\r
-            , "Out of memory",\r
-            javax.swing.JOptionPane.WARNING_MESSAGE);\r
+        javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+        {\r
+          public void run()\r
+          {\r
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                "Out of memory calculating conservation!!"\r
+                +\r
+                "\nSee help files for increasing Java Virtual Machine memory."\r
+                , "Out of memory",\r
+                javax.swing.JOptionPane.WARNING_MESSAGE);\r
+          }\r
+        });\r
+\r
         System.out.println("Conservation calculation: " + error);\r
         System.gc();\r
 \r
@@ -377,12 +410,20 @@ public class AlignViewport
 \r
       }catch(OutOfMemoryError error)\r
       {\r
-        javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-            "Out of memory calculating consensus!!"\r
-            +\r
-            "\nSee help files for increasing Java Virtual Machine memory."\r
-            , "Out of memory",\r
-            javax.swing.JOptionPane.WARNING_MESSAGE);\r
+        javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+        {\r
+          public void run()\r
+          {\r
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                "Out of memory calc45ulating consensus!!"\r
+                +\r
+                "\nSee help files for increasing Java Virtual Machine memory."\r
+                , "Out of memory",\r
+                javax.swing.JOptionPane.WARNING_MESSAGE);\r
+          }\r
+        });\r
+\r
+\r
         System.out.println("Consensus calculation: " + error);\r
         System.gc();\r
       }\r
@@ -584,6 +625,7 @@ public class AlignViewport
         java.awt.FontMetrics fm = c.getFontMetrics(font);\r
         setCharHeight(fm.getHeight());\r
         setCharWidth(fm.charWidth('M'));\r
+        validCharWidth = true;\r
     }\r
 \r
     /**\r
@@ -1060,7 +1102,6 @@ public class AlignViewport
       {\r
         globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);\r
       }\r
-\r
     }\r
 \r
     public boolean getIgnoreGapsConsensus()\r
@@ -1077,4 +1118,23 @@ public class AlignViewport
     {\r
       return isDataset;\r
     }\r
+\r
+    public void hideSequence(SequenceI seq)\r
+    {\r
+      alignment.getHiddenSequences().hideSequence(seq);\r
+      hasHiddenRows = true;\r
+    }\r
+\r
+    public void showSequence(int index)\r
+    {\r
+      alignment.getHiddenSequences().showSequence(index);\r
+\r
+      if(alignment.getHiddenSequences().getSize()<1)\r
+        hasHiddenRows = false;\r
+    }\r
+\r
+    public int adjustForHiddenSeqs(int alignmentIndex)\r
+    {\r
+      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);\r
+    }\r
 }\r