X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=8ec234d12128745ff90f873ed3fa50611d9448c0;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=77f881051b65ba97a967814bcfa5501159bc1b54;hpb=8dc84fa0ff3fc476c41b2027d3616ee1470f6fa7;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 77f8810..8ec234d 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -22,159 +22,240 @@ package jalview.io;
 import java.io.*;
 import jalview.datamodel.*;
 import java.util.*;
-import jalview.schemes.UserColourScheme;
 import java.net.URL;
+import jalview.schemes.*;
+import jalview.analysis.Conservation;
 
 
 public class AnnotationFile
 {
+  StringBuffer text = new StringBuffer(
+        "JALVIEW_ANNOTATION\n"
+        +"# Created: "
+      +new java.util.Date()+"\n\n");
 
-  public String printAnnotations(AlignmentAnnotation [] annotations)
+  public String printAnnotations(AlignmentAnnotation [] annotations,
+                                Vector groups)
   {
-    StringBuffer text = new StringBuffer(
-      "JALVIEW_ANNOTATION\n"
-      +"# Created: "
-      +new java.util.Date()+"\n\n");
+    if(annotations!=null)
+    {
+      AlignmentAnnotation row;
+      String comma;
+      SequenceI seqref = null;
 
-    AlignmentAnnotation row;
-    String comma;
-    String seqref = null;
+      StringBuffer colours = new StringBuffer();
+      StringBuffer graphLine = new StringBuffer();
 
-    StringBuffer colours = new StringBuffer();
-    StringBuffer graphLine = new StringBuffer();
+      Hashtable graphGroup = new Hashtable();
 
-    Hashtable graphGroup = new Hashtable();
+      java.awt.Color color;
 
-    java.awt.Color color;
+      for (int i = 0; i < annotations.length; i++)
+      {
+        row = annotations[i];
 
-    for(int i=0; i<annotations.length; i++)
-    {
-      row = annotations[i];
-      color = null;
+        if (!row.visible)
+          continue;
 
-      if( row.sequenceRef == null)
-        seqref = null;
+        color = null;
 
-      else if (seqref == null
-           || !seqref.equals(row.sequenceRef.getName()))
-      {
-        seqref = row.sequenceRef.getName();
-        text.append("\nSEQUENCE_REF\t" + seqref + "\n");
-      }
+        if (row.sequenceRef == null)
+        {
+          if (seqref != null)
+            text.append("\nSEQUENCE_REF\tALIGNMENT\n");
 
+          seqref = null;
+        }
 
-      if( row.graph == AlignmentAnnotation.NO_GRAPH)
-      {
+        else if (seqref == null || seqref != row.sequenceRef)
+        {
+          seqref = row.sequenceRef;
+          text.append("\nSEQUENCE_REF\t" + seqref.getName() + "\n");
+        }
+
+        if (row.graph == AlignmentAnnotation.NO_GRAPH)
+        {
           text.append("NO_GRAPH\t");
-      }
-      else
-      {
-        if( row.graph == AlignmentAnnotation.BAR_GRAPH)
-          text.append("BAR_GRAPH\t");
-        else if(row.graph == AlignmentAnnotation.LINE_GRAPH)
-          text.append("LINE_GRAPH\t");
+        }
+        else
+        {
+          if (row.graph == AlignmentAnnotation.BAR_GRAPH)
+            text.append("BAR_GRAPH\t");
+          else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+            text.append("LINE_GRAPH\t");
 
-        if(row.getThreshold()!=null)
+          if (row.getThreshold() != null)
             graphLine.append("GRAPHLINE\t"
                              + row.label + "\t"
                              + row.getThreshold().value + "\t"
                              + row.getThreshold().label + "\t"
                              + jalview.util.Format.getHexString(
-                                 row.getThreshold().colour)+"\n"
+                                 row.getThreshold().colour) + "\n"
                 );
 
-          if(row.graphGroup>-1)
+          if (row.graphGroup > -1)
           {
             String key = String.valueOf(row.graphGroup);
-            if(graphGroup.containsKey(key))
+            if (graphGroup.containsKey(key))
               graphGroup.put(key, graphGroup.get(key)
-                             +"\t"+row.label);
+                             + "\t" + row.label);
             else
               graphGroup.put(key, row.label);
           }
-      }
+        }
 
-      text.append(row.label+"\t");
+        text.append(row.label + "\t");
+        if (row.description != null)
+          text.append(row.description + "\t");
 
-      for(int j=0; j<row.annotations.length; j++)
-      {
-        if(row.annotations[j]!=null)
+        for (int j = 0; j < row.annotations.length; j++)
         {
-          comma = "";
-          if (row.annotations[j].secondaryStructure!=' ')
-          {
-            text.append(comma + row.annotations[j].secondaryStructure);
-            comma = ",";
-          }
-          if (row.annotations[j].displayCharacter.length() > 0 
-                  && !row.annotations[j].displayCharacter.equals(" "))
-              {
-                text.append(comma + row.annotations[j].displayCharacter);
-                comma = ",";
-              }
-          if (row.annotations[j].value!=0f)
+          if (seqref != null &&
+              jalview.util.Comparison.isGap(seqref.getCharAt(j)))
+            continue;
+
+          if (row.annotations[j] != null)
           {
-            color = row.annotations[j].colour;
-            text.append(comma + row.annotations[j].value);
+            comma = "";
+            if (row.annotations[j].secondaryStructure != ' ')
+            {
+              text.append(comma + row.annotations[j].secondaryStructure);
+              comma = ",";
+            }
+            if (row.annotations[j].displayCharacter.length() > 0
+                && !row.annotations[j].displayCharacter.equals(" "))
+            {
+              text.append(comma + row.annotations[j].displayCharacter);
+              comma = ",";
+            }
+
+            if (row.annotations[j] != null)
+            {
+              color = row.annotations[j].colour;
+              if (row.annotations[j].value != 0f)
+                text.append(comma + row.annotations[j].value);
+            }
           }
+          text.append("|");
+        }
+
+        text.append("\n");
+
+        if (color != null && color != java.awt.Color.black)
+        {
+          colours.append("COLOUR\t"
+                         + row.label + "\t"
+                         + jalview.util.Format.getHexString(color) + "\n");
         }
-        text.append("|");
+
       }
 
       text.append("\n");
 
-      if(color!=null && color!=java.awt.Color.black)
+      text.append(colours.toString());
+      text.append(graphLine.toString());
+      if (graphGroup.size() > 0)
       {
-        colours.append("COLOUR\t"
-                       +row.label+"\t"
-                       +jalview.util.Format.getHexString(color)+"\n");
+        text.append("COMBINE\t");
+        Enumeration en = graphGroup.elements();
+        while (en.hasMoreElements())
+        {
+          text.append(en.nextElement() + "\n");
+        }
       }
+    }
+
 
+    if(groups!=null)
+    {
+      printGroups(groups);
     }
 
-    text.append("\n");
+    return text.toString();
+  }
+
 
-    text.append(colours.toString());
-    text.append(graphLine.toString());
-    if(graphGroup.size()>0)
+  public void printGroups(Vector sequenceGroups)
+  {
+    SequenceGroup sg;
+    for (int i = 0; i < sequenceGroups.size(); i++)
     {
-      text.append("COMBINE\t");
-      Enumeration en = graphGroup.elements();
-      while(en.hasMoreElements())
+      sg = (SequenceGroup) sequenceGroups.elementAt(i);
+      text.append("SEQUENCE_GROUP\t"
+                  + sg.getName() + "\t"
+                  + (sg.getStartRes()+1) + "\t"
+                  + (sg.getEndRes()+1)  + "\t" + "-1\t");
+      for(int s=0; s<sg.getSize(); s++)
       {
-        text.append(en.nextElement()+"\n");
+        text.append(sg.getSequenceAt(s).getName()+"\t");
       }
-    }
 
-    return text.toString();
+      text.append("\nPROPERTIES\t"+sg.getName()+"\t");
+
+      if(sg.getDescription()!=null)
+        text.append("description="+sg.getDescription()+"\t");
+      if(sg.cs!=null)
+      {
+        text.append("colour="+ColourSchemeProperty.getColourName(sg.cs)+"\t");
+        if(sg.cs.getThreshold()!=0)
+          text.append("pidThreshold="+sg.cs.getThreshold());
+        if(sg.cs.conservationApplied())
+          text.append("consThreshold="+sg.cs.getConservationInc()+"\t");
+      }
+      text.append("outlineColour="+
+                  jalview.util.Format.getHexString(sg.getOutlineColour())+"\t");
+
+      text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");
+      text.append("displayText=" + sg.getDisplayText() + "\t");
+      text.append("colourText=" + sg.getColourText() + "\t");
+
+      if (sg.textColour != java.awt.Color.black)
+        text.append("textCol1=" +
+                    jalview.util.Format.getHexString(sg.textColour) + "\t");
+      if (sg.textColour2 != java.awt.Color.white)
+        text.append("textCol2=" +
+                    jalview.util.Format.getHexString(sg.textColour2) + "\t");
+      if(sg.thresholdTextColour!=0)
+      text.append("textColThreshold="+sg.thresholdTextColour);
+
+      text.append("\n\n");
+
+    }
   }
 
-  public boolean readAnnotationFile(AlignmentI al, String file)
+
+  SequenceI refSeq = null;
+  public boolean readAnnotationFile(AlignmentI al,
+                                    String file,
+                                    String protocol)
   {
     try
     {
       BufferedReader in = null;
-      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
-      if (is != null)
+      if (protocol.equals(AppletFormatAdapter.FILE))
       {
-        in = new BufferedReader(new java.io.InputStreamReader(is));
+        in = new BufferedReader(new FileReader(file));
       }
-      else
+      else if (protocol.equals(AppletFormatAdapter.URL))
       {
-        try
-        {
-          URL url = new URL(file);
-          in = new BufferedReader(new InputStreamReader(url.openStream()));
-        }
-        catch (java.net.MalformedURLException ex)
+        URL url = new URL(file);
+        in = new BufferedReader(new InputStreamReader(url.openStream()));
+      }
+     else if (protocol.equals(AppletFormatAdapter.PASTE))
+      {
+        in = new BufferedReader(new StringReader(file));
+      }
+      else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+      {
+        java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+        if (is != null)
         {
-          in = new BufferedReader(new FileReader(file));
+          in = new BufferedReader(new java.io.InputStreamReader(is));
         }
-      }
+    }
 
       String line, label, description, token;
       int graphStyle, index;
-      SequenceI refSeq = null;
       int refSeqIndex = 1;
       int existingAnnotations = 0;
       if(al.getAlignmentAnnotation()!=null)
@@ -221,24 +302,29 @@ public class AnnotationFile
           continue;
         }
 
-        if(token.equalsIgnoreCase("COMBINE") )
+        else if(token.equalsIgnoreCase("COMBINE") )
         {
           combineAnnotations(al, st);
           continue;
         }
 
-        if (token.equalsIgnoreCase("GRAPHLINE"))
+        else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
           continue;
         }
 
 
-        if(token.equalsIgnoreCase("SEQUENCE_REF") )
+        else if(token.equalsIgnoreCase("SEQUENCE_REF") )
         {
           refSeq = al.findName(st.nextToken());
           try{
             refSeqIndex = Integer.parseInt(st.nextToken());
+            if(refSeqIndex<1)
+            {
+              refSeqIndex = 1;
+              System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+            }
           }
           catch(Exception ex)
           {
@@ -248,9 +334,26 @@ public class AnnotationFile
           continue;
         }
 
+        else if(token.equalsIgnoreCase("SEQUENCE_GROUP"))
+        {
+          addGroup(al, st);
+          continue;
+        }
+
+        else if(token.equalsIgnoreCase("PROPERTIES"))
+        {
+          addProperties(al, st);
+          continue;
+        }
+
 
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
-        label = description = st.nextToken();
+        label = st.nextToken();
+
+        if(st.countTokens()>1)
+          description = st.nextToken();
+        else
+          description = null;
 
         line = st.nextToken();
 
@@ -307,7 +410,7 @@ public class AnnotationFile
 
   Annotation parseAnnotation(String string)
   {
-    String desc = "", displayChar="";
+    String desc = null, displayChar="";
     char ss = ' '; // secondaryStructure
     float value = 0;
     boolean parsedValue = false;
@@ -325,6 +428,7 @@ public class AnnotationFile
           displayChar = token;
           value = new Float(token).floatValue();
           parsedValue = true;
+          continue;
         }catch(NumberFormatException ex){}
       }
 
@@ -336,11 +440,21 @@ public class AnnotationFile
         if(displayChar.equals(token.substring(0,1)))
           displayChar = "";
       }
-      else if(desc.length()<1)
+      else if(desc==null)
         desc = token;
 
     }
 
+    if(desc == null)
+      desc = value+"";
+
+    if(displayChar.length()>1 && desc.length()==1)
+    {
+      String tmp = displayChar;
+      displayChar = desc;
+      desc = tmp;
+    }
+
     return new Annotation(displayChar, desc, ss, value);
   }
 
@@ -418,6 +532,145 @@ public class AnnotationFile
     }
 
     annotation.setThreshold(new GraphLine(value, label, colour));
+  }
+
+  void addGroup(AlignmentI al, StringTokenizer st)
+  {
+    SequenceGroup sg = new SequenceGroup();
+    sg.setName(st.nextToken());
+    sg.setStartRes(Integer.parseInt(st.nextToken())-1);
+    sg.setEndRes(Integer.parseInt(st.nextToken())-1);
+
+    String index = st.nextToken();
+    if(index.equals("-1"))
+    {
+      while (st.hasMoreElements())
+      {
+        sg.addSequence(al.findName(st.nextToken()), false);
+      }
+    }
+    else
+    {
+      StringTokenizer st2 = new StringTokenizer(index, ",");
+
+      while (st2.hasMoreTokens())
+      {
+        String tmp = st2.nextToken();
+        if (tmp.equals("*"))
+        {
+          for (int i = 0; i < al.getHeight(); i++)
+          {
+            sg.addSequence(al.getSequenceAt(i), false);
+          }
+        }
+        else if (tmp.indexOf("-") >= 0)
+        {
+          StringTokenizer st3 = new StringTokenizer(tmp, "-");
+
+          int start = (Integer.parseInt(st3.nextToken()));
+          int end = (Integer.parseInt(st3.nextToken()));
+
+          if (end > start)
+            for (int i = start; i <= end; i++)
+              sg.addSequence(al.getSequenceAt(i-1), false);
+        }
+        else
+        {
+          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp)-1 ), false);
+        }
+      }
+    }
 
+    if(refSeq!=null)
+    {
+      sg.setStartRes( refSeq.findIndex( sg.getStartRes()+1 )-1 );
+      sg.setEndRes(   refSeq.findIndex( sg.getEndRes() +1) -1 );
+    }
+
+    if(sg.getSize()>0)
+    {
+      al.addGroup(sg);
+    }
+  }
+
+  void addProperties(AlignmentI al, StringTokenizer st)
+  {
+
+    //So far we have only added groups to the annotationHash,
+    //the idea is in the future properties can be added to
+    //alignments, other annotations etc
+    if(al.getGroups()==null)
+      return;
+    SequenceGroup sg = null;
+
+    String name = st.nextToken();
+
+    Vector groups = al.getGroups();
+    for(int i=0; i<groups.size(); i++)
+    {
+      sg = (SequenceGroup)groups.elementAt(i);
+      if(sg.getName().equals(name))
+        break;
+      else
+        sg = null;
+    }
+
+    if(sg!=null)
+    {
+      String keyValue, key, value;
+      while(st.hasMoreTokens())
+      {
+        keyValue = st.nextToken();
+        key = keyValue.substring(0,keyValue.indexOf("="));
+        value=keyValue.substring(keyValue.indexOf("=")+1);
+
+        if(key.equalsIgnoreCase("description"))
+          sg.setDescription(value);
+        else if(key.equalsIgnoreCase("colour"))
+          sg.cs = ColourSchemeProperty.getColour(al, value);
+        else if (key.equalsIgnoreCase("pidThreshold"))
+        {
+          sg.cs.setThreshold(Integer.parseInt(value), true);
+
+        }
+        else if (key.equalsIgnoreCase("consThreshold"))
+        {
+          sg.cs.setConservationInc(Integer.parseInt(value));
+          Conservation c = new Conservation("Group",
+                    ResidueProperties.propHash, 3,
+                    sg.getSequences(null),
+                    sg.getStartRes(),
+                    sg.getEndRes() + 1);
+
+            c.calculate();
+            c.verdict(false, 25);
+
+            sg.cs.setConservation(c);
+
+        }
+        else if (key.equalsIgnoreCase("outlineColour"))
+         {
+           sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+         }
+        else if (key.equalsIgnoreCase("displayBoxes"))
+         sg.setDisplayBoxes( Boolean.valueOf(value).booleanValue() );
+        else if (key.equalsIgnoreCase("displayText"))
+         sg.setDisplayText( Boolean.valueOf(value).booleanValue() );
+        else if (key.equalsIgnoreCase("colourText"))
+         sg.setColourText( Boolean.valueOf(value).booleanValue() );
+        else if (key.equalsIgnoreCase("textCol1"))
+         {
+           sg.textColour = new UserColourScheme(value).findColour('A');
+         }
+        else if (key.equalsIgnoreCase("textCol2"))
+        {
+          sg.textColour2 = new UserColourScheme(value).findColour('A');
+        }
+        else if (key.equalsIgnoreCase("textColThreshold"))
+         sg.thresholdTextColour = Integer.parseInt(value);
+
+       sg.recalcConservation();
+      }
+    }
   }
 }