remove mentions of non-functional RNAInteraction colourscheme

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 700c229..04e86fa 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,18 +1,18 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
  * This file is part of Jalview.\r
- *\r
+ * \r
  * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
+ * modify it under the terms of the GNU General Public License \r
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- *\r
- * Jalview is distributed in the hope that it will be useful, but\r
- * WITHOUT ANY WARRANTY; without even the implied warranty\r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR\r
+ *  \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
  * PURPOSE.  See the GNU General Public License for more details.\r
- *\r
+ * \r
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package jalview.appletgui;\r
@@ -52,6 +52,7 @@ import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;\r
 import jalview.schemes.PurinePyrimidineColourScheme;\r
 import jalview.schemes.RNAHelicesColourChooser;\r
+import jalview.schemes.RNAInteractionColourScheme;\r
 import jalview.schemes.ResidueProperties;\r
 import jalview.schemes.StrandColourScheme;\r
 import jalview.schemes.TCoffeeColourScheme;\r
@@ -92,6 +93,15 @@ import java.util.List;
 import java.util.StringTokenizer;\r
 import java.util.Vector;\r
 \r
+import javax.xml.parsers.ParserConfigurationException;\r
+\r
+import org.xml.sax.SAXException;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
+\r
 public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
         ItemListener, KeyListener\r
 {\r
@@ -208,6 +218,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       RNAHelixColour.setEnabled(false);\r
       purinePyrimidineColour.setEnabled(false);\r
     }\r
+\r
     // Some JVMS send keyevents to Top frame or lowest panel,\r
     // Havent worked out why yet. So add to both this frame and seqCanvas for\r
     // now\r
@@ -1025,6 +1036,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       changeColour(new PurinePyrimidineColourScheme());\r
     }\r
+\r
     else if (source == RNAHelixColour)\r
     {\r
       new RNAHelicesColourChooser(viewport, alignPanel);\r
@@ -2698,9 +2710,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         g.drawString("Build date: " + builddate, x, y += fh);\r
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
         g.drawString(\r
-                "Authors:  Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",\r
+                "Authors:  Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",\r
                 x, y += fh * 1.5);\r
-        g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);\r
+        g.drawString(\r
+                "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",\r
+                x + 50, y += fh + 8);\r
         g.drawString(\r
                 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",\r
                 x, y += fh);\r
@@ -2825,6 +2839,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 \r
   MenuItem purinePyrimidineColour = new MenuItem();\r
 \r
+  MenuItem RNAInteractionColour = new MenuItem();\r
+\r
   MenuItem RNAHelixColour = new MenuItem();\r
 \r
   MenuItem userDefinedColour = new MenuItem();\r
@@ -3028,6 +3044,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     buriedColour.addActionListener(this);\r
     purinePyrimidineColour.setLabel("Purine/Pyrimidine");\r
     purinePyrimidineColour.addActionListener(this);\r
+    RNAInteractionColour.setLabel("Purine/Pyrimidine");\r
+    RNAInteractionColour.addActionListener(this);\r
     RNAHelixColour.setLabel("by RNA Helices");\r
     RNAHelixColour.addActionListener(this);\r
     userDefinedColour.setLabel("User Defined...");\r
@@ -3170,8 +3188,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     showGroupConservation.addItemListener(this);\r
     showConsensusHistogram.addItemListener(this);\r
     showSequenceLogo.addItemListener(this);\r
-    normSequenceLogo.addItemListener(this);\r
-\r
     applyAutoAnnotationSettings.addItemListener(this);\r
     formatMenu.setLabel("Format");\r
     selectMenu.setLabel("Select");\r
@@ -3252,6 +3268,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(buriedColour);\r
     colourMenu.add(nucleotideColour);\r
     colourMenu.add(purinePyrimidineColour);\r
+    //    colourMenu.add(RNAInteractionColour);\r
     colourMenu.add(tcoffeeColour);\r
     colourMenu.add(userDefinedColour);\r
     colourMenu.addSeparator();\r
@@ -3704,8 +3721,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    *          File/URL/T-COFFEE score file contents\r
    * @throws IOException\r
    * @return true if alignment was annotated with data from source\r
+   * @throws SAXException\r
+   * @throws ParserConfigurationException\r
+   * @throws ExceptionFileFormatOrSyntax\r
+   * @throws ExceptionLoadingFailed\r
+   * @throws ExceptionPermissionDenied\r
+   * @throws InterruptedException\r
+   * @throws ExceptionUnmatchedClosingParentheses\r
    */\r
-  public boolean loadScoreFile(String source) throws IOException\r
+  public boolean loadScoreFile(String source) throws Exception\r
   {\r
 \r
     TCoffeeScoreFile file = new TCoffeeScoreFile(source,\r