ModellerOutput set in preferences

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 9702a92..eb503d5 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -213,6 +213,7 @@ public class Cache
 \r
         //LOAD USERDEFINED COLOURS\r
         jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));\r
+        jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);\r
     }\r
 \r
 \r

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8cbe03f..9ac8acf 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -150,7 +150,10 @@ public class Preferences extends GPreferences
         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
 \r
+        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
+\r
         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
 \r
   /****************************************************\r
    * Set up Connections\r
@@ -278,10 +281,13 @@ public class Preferences extends GPreferences
         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
+        jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
 \r
         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));\r
-\r
+        Cache.applicationProperties.setProperty("PAD_GAPS",\r
+                                                Boolean.toString(padGaps.isSelected()));\r
         Cache.saveProperties();\r
         try\r
         {\r

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 6d6e525..b958456 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -26,6 +26,8 @@ import jalview.datamodel.*;
 public class PIRFile\r
     extends AlignFile\r
 {\r
+  public static boolean useModellerOutput = false;\r
+\r
   Vector words = new Vector(); //Stores the words in a line after splitting\r
 \r
   public PIRFile()\r
@@ -47,6 +49,7 @@ public class PIRFile
   {\r
       StringBuffer sequence;\r
       String line = null;\r
+      ModellerDescription md;\r
 \r
       while ( (line = nextLine()) != null)\r
       {\r
@@ -93,8 +96,9 @@ public class PIRFile
           }\r
 \r
           seqs.addElement(newSeq);\r
-          ModellerDescription md = new ModellerDescription(newSeq.\r
-              getDescription());\r
+\r
+          md = new ModellerDescription(newSeq.\r
+                getDescription());\r
           md.updateSequenceI(newSeq);\r
         }\r
       }\r
@@ -111,17 +115,28 @@ public class PIRFile
     int len = 72;\r
     StringBuffer out = new StringBuffer();\r
     int i = 0;\r
+    ModellerDescription md;\r
 \r
     while ( (i < s.length) && (s[i] != null))\r
     {\r
       String seq = s[i].getSequence();\r
       seq = seq + "*";\r
 \r
+\r
       if (is_NA)\r
       {\r
-        // modeller doesn't really do nucleotides, so we don't do anything fancy\r
-        // Nucleotide sequence tags should have a >DL; prefix\r
-        out.append(">N1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N\r
+          // modeller doesn't really do nucleotides, so we don't do anything fancy\r
+          // Official tags area as follows, for now we'll use P1 and DL\r
+          // Protein (complete) P1\r
+          // Protein (fragment) F1\r
+          // DNA (linear) Dl\r
+          // DNA (circular) DC\r
+          // RNA (linear) RL\r
+          // RNA (circular) RC\r
+          // tRNA N3\r
+          // other functional RNA N1\r
+\r
+        out.append(">N1;" + s[i].getName() + "\n");\r
         if (s[i].getDescription() == null)\r
         {\r
           out.append(s[i].getName() + " " +\r
@@ -135,9 +150,23 @@ public class PIRFile
       }\r
       else\r
       {\r
-        out.append(">P1;" + s[i].getName() + "\n");\r
-        ModellerDescription md = new ModellerDescription(s[i]);\r
-        out.append(md.getDescriptionLine() + "\n");\r
+\r
+       if(useModellerOutput)\r
+       {\r
+         out.append(">P1;" + s[i].getName() + "\n");\r
+         md = new ModellerDescription(s[i]);\r
+         out.append(md.getDescriptionLine() + "\n");\r
+       }\r
+       else\r
+       {\r
+         out.append(">P1;" + printId(s[i]) + "\n");\r
+         if (s[i].getDescription() != null)\r
+           out.append(s[i].getDescription() + "\n");\r
+         else\r
+           out.append(s[i].getName() + " "\r
+                      + (s[i].getEnd() - s[i].getStart() + 1)\r
+                      + " residues\n");\r
+       }\r
       }\r
       int nochunks = (seq.length() / len) + 1;\r
 \r

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 58c7743..8a51aee 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -106,6 +106,8 @@ public class GPreferences extends JPanel
   protected JCheckBox smoothFont = new JCheckBox();\r
   JPanel calcTab = new JPanel();\r
   protected JCheckBox autoCalculateConsCheck = new JCheckBox();\r
+  protected JCheckBox padGaps = new JCheckBox();\r
+  protected JCheckBox modellerOutput = new JCheckBox();\r
   /**\r
      * Creates a new GPreferences object.\r
      */\r
@@ -360,8 +362,15 @@ public class GPreferences extends JPanel
     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);\r
     smoothFont.setText("Smooth Font");\r
     calcTab.setLayout(null);\r
+    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
     autoCalculateConsCheck.setText("AutoCalculate Consensus");\r
-    autoCalculateConsCheck.setBounds(new Rectangle(16, 29, 209, 23));\r
+    autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));\r
+    padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    padGaps.setText("Pad gaps when editing");\r
+    padGaps.setBounds(new Rectangle(22, 94, 168, 23));\r
+    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    modellerOutput.setText("Use Modeller Output");\r
+    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));\r
     jPanel2.add(fullScreen);\r
 \r
     jPanel2.add(annotations);\r
@@ -444,8 +453,10 @@ public class GPreferences extends JPanel
     jPanel11.add(pfamjv);\r
     jPanel11.add(pileupjv);\r
     jPanel11.add(pirjv);\r
+    exportTab.add(modellerOutput);\r
     tabbedPane.add(calcTab, "Calculations");\r
     calcTab.add(autoCalculateConsCheck);\r
+    calcTab.add(padGaps);\r
 \r
     exportTab.add(epsLabel);\r
     exportTab.add(epsRendering);\r