From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 7 Apr 2006 12:52:29 +0000 (+0000)
Subject: ModellerOutput set in preferences
X-Git-Tag: Release_2_08~39
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=38299bef6dfd4b713f615781e631dcb66e1155f2;p=jalview.git

ModellerOutput set in preferences
---

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 9702a92..eb503d5 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -213,6 +213,7 @@ public class Cache
 
         //LOAD USERDEFINED COLOURS
         jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS"));
+        jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
     }
 
 
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8cbe03f..9ac8acf 100755
--- 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) );
         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
 
+        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+
         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
 
   /****************************************************
    * Set up Connections
@@ -278,10 +281,13 @@ public class Preferences extends GPreferences
         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
+        jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));
-
+        Cache.applicationProperties.setProperty("PAD_GAPS",
+                                                Boolean.toString(padGaps.isSelected()));
         Cache.saveProperties();
         try
         {
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 6d6e525..b958456 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -26,6 +26,8 @@ import jalview.datamodel.*;
 public class PIRFile
     extends AlignFile
 {
+  public static boolean useModellerOutput = false;
+
   Vector words = new Vector(); //Stores the words in a line after splitting
 
   public PIRFile()
@@ -47,6 +49,7 @@ public class PIRFile
   {
       StringBuffer sequence;
       String line = null;
+      ModellerDescription md;
 
       while ( (line = nextLine()) != null)
       {
@@ -93,8 +96,9 @@ public class PIRFile
           }
 
           seqs.addElement(newSeq);
-          ModellerDescription md = new ModellerDescription(newSeq.
-              getDescription());
+
+          md = new ModellerDescription(newSeq.
+                getDescription());
           md.updateSequenceI(newSeq);
         }
       }
@@ -111,17 +115,28 @@ public class PIRFile
     int len = 72;
     StringBuffer out = new StringBuffer();
     int i = 0;
+    ModellerDescription md;
 
     while ( (i < s.length) && (s[i] != null))
     {
       String seq = s[i].getSequence();
       seq = seq + "*";
 
+
       if (is_NA)
       {
-        // modeller doesn't really do nucleotides, so we don't do anything fancy
-        // Nucleotide sequence tags should have a >DL; prefix
-        out.append(">N1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N
+          // modeller doesn't really do nucleotides, so we don't do anything fancy
+          // Official tags area as follows, for now we'll use P1 and DL
+          // Protein (complete) P1
+          // Protein (fragment) F1
+          // DNA (linear) Dl
+          // DNA (circular) DC
+          // RNA (linear) RL
+          // RNA (circular) RC
+          // tRNA N3
+          // other functional RNA N1
+
+        out.append(">N1;" + s[i].getName() + "\n");
         if (s[i].getDescription() == null)
         {
           out.append(s[i].getName() + " " +
@@ -135,9 +150,23 @@ public class PIRFile
       }
       else
       {
-        out.append(">P1;" + s[i].getName() + "\n");
-        ModellerDescription md = new ModellerDescription(s[i]);
-        out.append(md.getDescriptionLine() + "\n");
+
+       if(useModellerOutput)
+       {
+         out.append(">P1;" + s[i].getName() + "\n");
+         md = new ModellerDescription(s[i]);
+         out.append(md.getDescriptionLine() + "\n");
+       }
+       else
+       {
+         out.append(">P1;" + printId(s[i]) + "\n");
+         if (s[i].getDescription() != null)
+           out.append(s[i].getDescription() + "\n");
+         else
+           out.append(s[i].getName() + " "
+                      + (s[i].getEnd() - s[i].getStart() + 1)
+                      + " residues\n");
+       }
       }
       int nochunks = (seq.length() / len) + 1;
 
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 58c7743..8a51aee 100755
--- 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();
   JPanel calcTab = new JPanel();
   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
+  protected JCheckBox padGaps = new JCheckBox();
+  protected JCheckBox modellerOutput = new JCheckBox();
   /**
      * Creates a new GPreferences object.
      */
@@ -360,8 +362,15 @@ public class GPreferences extends JPanel
     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
     smoothFont.setText("Smooth Font");
     calcTab.setLayout(null);
+    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     autoCalculateConsCheck.setText("AutoCalculate Consensus");
-    autoCalculateConsCheck.setBounds(new Rectangle(16, 29, 209, 23));
+    autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
+    padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    padGaps.setText("Pad gaps when editing");
+    padGaps.setBounds(new Rectangle(22, 94, 168, 23));
+    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    modellerOutput.setText("Use Modeller Output");
+    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
     jPanel2.add(fullScreen);
 
     jPanel2.add(annotations);
@@ -444,8 +453,10 @@ public class GPreferences extends JPanel
     jPanel11.add(pfamjv);
     jPanel11.add(pileupjv);
     jPanel11.add(pirjv);
+    exportTab.add(modellerOutput);
     tabbedPane.add(calcTab, "Calculations");
     calcTab.add(autoCalculateConsCheck);
+    calcTab.add(padGaps);
 
     exportTab.add(epsLabel);
     exportTab.add(epsRendering);