Conservation colour scheme is no more

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index db1f9c9..6138257 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -27,6 +27,8 @@ import jalview.io.*;
 import java.awt.*;\r
 import java.awt.event.*;\r
 import java.util.*;\r
+import java.io.InputStreamReader;\r
+import java.io.BufferedReader;\r
 \r
 public class AlignFrame\r
     extends GAlignFrame\r
@@ -489,7 +491,7 @@ public class AlignFrame
     sg.setEndRes(viewport.alignment.getWidth());\r
     viewport.setSelectionGroup(sg);\r
     alignPanel.repaint();\r
-    PaintRefresher.Refresh(null);\r
+    PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
@@ -497,7 +499,7 @@ public class AlignFrame
     viewport.setSelectionGroup(null);\r
     viewport.getColumnSelection().clear();\r
     viewport.setSelectionGroup(null);\r
-    PaintRefresher.Refresh(null);\r
+    PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
@@ -508,7 +510,7 @@ public class AlignFrame
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
     }\r
 \r
-    PaintRefresher.Refresh(null);\r
+    PaintRefresher.Refresh(null, viewport.alignment);\r
   }\r
 \r
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
@@ -806,21 +808,17 @@ public class AlignFrame
     {\r
       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 \r
-      if (cs instanceof ResidueColourScheme)\r
-      {\r
-        ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-      }\r
+      cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 \r
       viewport.setGlobalColourScheme(cs);\r
     }\r
-    else if (cs instanceof ResidueColourScheme)\r
+    else\r
     {\r
-      ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+      cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
     }\r
 \r
     if (viewport.getConservationSelected())\r
     {\r
-      ConservationColourScheme ccs = null;\r
 \r
       Alignment al = (Alignment) viewport.alignment;\r
       Conservation c = new Conservation("All",\r
@@ -831,13 +829,13 @@ public class AlignFrame
       c.calculate();\r
       c.verdict(false, viewport.ConsPercGaps);\r
 \r
-      ccs = new ConservationColourScheme(c, cs);\r
+      cs.setConservation(c);\r
 \r
       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
-      ccs.setConsensus(viewport.vconsensus);\r
-      viewport.setGlobalColourScheme(ccs);\r
+      cs.setConsensus(viewport.vconsensus);\r
+      viewport.setGlobalColourScheme(cs);\r
 \r
-      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
+      SliderPanel.setConservationSlider(alignPanel, cs, "Background");\r
 \r
     }\r
     else\r
@@ -883,10 +881,7 @@ public class AlignFrame
 \r
         if (viewport.getAbovePIDThreshold())\r
         {\r
-          if (sg.cs instanceof ResidueColourScheme)\r
-          {\r
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
-          }\r
+          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 \r
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
         }\r
@@ -899,11 +894,10 @@ public class AlignFrame
                                             viewport.alignment.getWidth() - 1);\r
           c.calculate();\r
           c.verdict(false, viewport.ConsPercGaps);\r
-          ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 \r
           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
-          ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
-          sg.cs = ccs;\r
+          cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+          sg.cs = cs;\r
         }\r
         else\r
         {\r
@@ -957,15 +951,7 @@ public class AlignFrame
     viewport.setAbovePIDThreshold(false);\r
     abovePIDThreshold.setState(false);\r
 \r
-    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-    if (cs instanceof ConservationColourScheme)\r
-    {\r
-      changeColour( ( (ConservationColourScheme) cs).cs);\r
-    }\r
-    else\r
-    {\r
-      changeColour(cs);\r
-    }\r
+    changeColour(viewport.getGlobalColourScheme());\r
 \r
     modifyConservation_actionPerformed(null);\r
   }\r
@@ -977,16 +963,7 @@ public class AlignFrame
     conservationMenuItem.setState(false);\r
     viewport.setConservationSelected(false);\r
 \r
-    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
-    if (cs instanceof ConservationColourScheme)\r
-    {\r
-      changeColour( ( (ConservationColourScheme) cs).cs);\r
-    }\r
-    else\r
-    {\r
-      changeColour(cs);\r
-    }\r
+    changeColour(viewport.getGlobalColourScheme());\r
 \r
     modifyPID_actionPerformed(null);\r
   }\r
@@ -1169,9 +1146,13 @@ public class AlignFrame
 \r
   protected void about_actionPerformed(ActionEvent e)\r
   {\r
-    class AboutPanel\r
-        extends Canvas\r
+\r
+    class AboutPanel extends Canvas\r
     {\r
+      String version;\r
+      public AboutPanel(String version)\r
+      { this.version = version; }\r
+\r
       public void paint(Graphics g)\r
       {\r
         g.setColor(Color.white);\r
@@ -1182,7 +1163,7 @@ public class AlignFrame
         int y = 5, x = 7;\r
         g.setColor(Color.black);\r
         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
-        g.drawString("JalView - Release 2.02", 200, y += fh);\r
+        g.drawString("Jalview - Release "+version, 200, y += fh);\r
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
                      x, y += fh * 2);\r
@@ -1198,8 +1179,32 @@ public class AlignFrame
       }\r
     }\r
 \r
+    String version = "test";\r
+    java.net.URL url = getClass().getResource("/.build_properties");\r
+    if (url != null)\r
+    {\r
+      try\r
+      {\r
+        BufferedReader reader = new BufferedReader(new InputStreamReader(\r
+            url.openStream()));\r
+        String line;\r
+        while ( (line = reader.readLine()) != null)\r
+        {\r
+          if (line.indexOf("VERSION") > -1)\r
+          {\r
+            version = line.substring(line.indexOf("=") + 1);\r
+          }\r
+        }\r
+      }\r
+      catch (Exception ex)\r
+      {\r
+        ex.printStackTrace();\r
+      }\r
+    }\r
+\r
+\r
     Frame frame = new Frame();\r
-    frame.add(new AboutPanel());\r
+    frame.add(new AboutPanel(version));\r
     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
 \r
   }\r