X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ae34f6b8c1b42e7d9b3b4a5fbe12bbd5ae262ec4;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=773633238ace37a835129e194cc4593d3fefc9cd;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 7736332..ae34f6b 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,13 +20,34 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.ColorUtils;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.InputStreamReader;
+import java.io.StringReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 public class AnnotationFile
 {
@@ -67,18 +88,18 @@ public class AnnotationFile
   }
 
   /**
-   * convenience method for pre-2.4 feature files which have no view, hidden
+   * convenience method for pre-2.9 annotation files which have no view, hidden
    * columns or hidden row keywords.
    * 
    * @param annotations
    * @param list
    * @param properties
-   * @return feature file as a string.
+   * @return annotation file as a string.
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
           List<SequenceGroup> list, Hashtable properties)
   {
-    return printAnnotations(annotations, list, properties, null);
+    return printAnnotations(annotations, list, properties, null, null, null);
 
   }
 
@@ -119,10 +140,56 @@ public class AnnotationFile
    * @return annotation file
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
-          List<SequenceGroup> list, Hashtable properties, ViewDef[] views)
+          List<SequenceGroup> list, Hashtable properties,
+          ColumnSelection cs, AlignmentI al, ViewDef view)
   {
-    // TODO: resolve views issue : annotationFile could contain visible region,
-    // or full data + hidden region specifications for a view.
+    if (view != null)
+    {
+      if (view.viewname != null)
+      {
+        text.append("VIEW_DEF\t" + view.viewname + "\n");
+      }
+      if (list == null)
+      {
+        list = view.visibleGroups;
+      }
+      if (cs == null)
+      {
+        cs = view.hiddencols;
+      }
+      if (al == null)
+      {
+        // add hidden rep sequences.
+      }
+    }
+    // first target - store and restore all settings for a view.
+    if (al != null && al.hasSeqrep())
+    {
+      text.append("VIEW_SETREF\t" + al.getSeqrep().getName() + "\n");
+    }
+    if (cs != null && cs.hasHiddenColumns())
+    {
+      text.append("VIEW_HIDECOLS\t");
+      List<int[]> hc = cs.getHiddenColumns();
+      boolean comma = false;
+      for (int[] r : hc)
+      {
+        if (!comma)
+        {
+          comma = true;
+        }
+        else
+        {
+          text.append(",");
+        }
+        text.append(r[0]);
+        text.append("-");
+        text.append(r[1]);
+      }
+      text.append("\n");
+    }
+    // TODO: allow efficient recovery of annotation data shown in several
+    // different views
     if (annotations != null)
     {
       boolean oneColour = true;
@@ -174,7 +241,7 @@ public class AnnotationFile
                     && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
                     .equals(" "));
             hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
-            hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
+            hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
             // be
             // rendered..
             hasText |= (row.annotations[j].description != null && row.annotations[j].description
@@ -227,8 +294,7 @@ public class AnnotationFile
             }
             else
             {
-              graphGroup_refs.put(key, new Object[]
-              { refSeq, refGroup });
+              graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
               graphGroup.put(key, row.label);
             }
           }
@@ -264,13 +330,13 @@ public class AnnotationFile
             }
             if (hasValues)
             {
-              if (row.annotations[j].value != Float.NaN)
+              if (!Float.isNaN(row.annotations[j].value))
               {
                 text.append(comma + row.annotations[j].value);
               }
               else
               {
-                System.err.println("Skipping NaN - not valid value.");
+                // System.err.println("Skipping NaN - not valid value.");
                 text.append(comma + 0f);// row.annotations[j].value);
               }
               comma = ",";
@@ -320,7 +386,9 @@ public class AnnotationFile
         }
 
         if (row.hasScore())
+        {
           text.append("\t" + row.score);
+        }
 
         text.append(newline);
 
@@ -403,7 +471,9 @@ public class AnnotationFile
         text.append(properties.get(key));
       }
       // TODO: output alignment visualization settings here if required
-
+      // iterate through one or more views, defining, marking columns and rows
+      // as visible/hidden, and emmitting view properties.
+      // View specific annotation is
     }
 
     return text.toString();
@@ -512,7 +582,7 @@ public class AnnotationFile
       if (sg.cs != null)
       {
         text.append("colour=");
-        text.append(ColourSchemeProperty.getColourName(sg.cs));
+        text.append(sg.cs.toString());
         text.append("\t");
         if (sg.cs.getThreshold() != 0)
         {
@@ -590,26 +660,50 @@ public class AnnotationFile
 
   String refSeqId = null;
 
+  public boolean annotateAlignmentView(AlignViewportI viewport,
+          String file, DataSourceType protocol)
+  {
+    ColumnSelection colSel = viewport.getColumnSelection();
+    if (colSel == null)
+    {
+      colSel = new ColumnSelection();
+    }
+    boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+            file, protocol);
+    if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+    {
+      viewport.setColumnSelection(colSel);
+    }
+
+    return rslt;
+  }
+
   public boolean readAnnotationFile(AlignmentI al, String file,
-          String protocol)
+          DataSourceType sourceType)
+  {
+    return readAnnotationFile(al, null, file, sourceType);
+  }
+
+  public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+          String file, DataSourceType sourceType)
   {
     BufferedReader in = null;
     try
     {
-      if (protocol.equals(AppletFormatAdapter.FILE))
+      if (sourceType == DataSourceType.FILE)
       {
         in = new BufferedReader(new FileReader(file));
       }
-      else if (protocol.equals(AppletFormatAdapter.URL))
+      else if (sourceType == DataSourceType.URL)
       {
         URL url = new URL(file);
         in = new BufferedReader(new InputStreamReader(url.openStream()));
       }
-      else if (protocol.equals(AppletFormatAdapter.PASTE))
+      else if (sourceType == DataSourceType.PASTE)
       {
         in = new BufferedReader(new StringReader(file));
       }
-      else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+      else if (sourceType == DataSourceType.CLASSLOADER)
       {
         java.io.InputStream is = getClass().getResourceAsStream("/" + file);
         if (is != null)
@@ -619,7 +713,7 @@ public class AnnotationFile
       }
       if (in != null)
       {
-        return parseAnnotationFrom(al, in);
+        return parseAnnotationFrom(al, colSel, in);
       }
 
     } catch (Exception ex)
@@ -642,8 +736,8 @@ public class AnnotationFile
 
   private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
 
-  public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
-          throws Exception
+  public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+          BufferedReader in) throws Exception
   {
     nlinesread = 0;
     ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
@@ -736,8 +830,8 @@ public class AnnotationFile
         else if (token.equalsIgnoreCase(COMBINE))
         {
           // keep a record of current state and resolve groupRef at end
-          combineAnnotation_calls.add(new Object[]
-          { st, refSeq, groupRef });
+          combineAnnotation_calls
+                  .add(new Object[] { st, refSeq, groupRef });
           modified = true;
           continue;
         }
@@ -750,8 +844,8 @@ public class AnnotationFile
         else if (token.equalsIgnoreCase(GRAPHLINE))
         {
           // resolve at end
-          deferredAnnotation_calls.add(new Object[]
-          { GRAPHLINE, st, refSeq, groupRef });
+          deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
+              refSeq, groupRef });
           modified = true;
           continue;
         }
@@ -834,6 +928,58 @@ public class AnnotationFile
           modified = true;
           continue;
         }
+        // else if (token.equalsIgnoreCase("VIEW_DEF"))
+        // {
+        // addOrSetView(al,st);
+        // modified = true;
+        // continue;
+        // }
+        else if (token.equalsIgnoreCase("VIEW_SETREF"))
+        {
+          if (refSeq != null)
+          {
+            al.setSeqrep(refSeq);
+          }
+          modified = true;
+          continue;
+        }
+        else if (token.equalsIgnoreCase("VIEW_HIDECOLS"))
+        {
+          if (st.hasMoreTokens())
+          {
+            if (colSel == null)
+            {
+              colSel = new ColumnSelection();
+            }
+            parseHideCols(colSel, st.nextToken());
+          }
+          modified = true;
+          continue;
+        }
+        else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
+        {
+          SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
+          if (sr == null)
+          {
+            sr = al.getSequenceAt(0);
+          }
+          if (sr != null)
+          {
+            if (colSel == null)
+            {
+              System.err
+                      .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+                              + line);
+            }
+            else
+            {
+              // consider deferring this till after the file has been parsed ?
+              colSel.hideInsertionsFor(sr);
+            }
+          }
+          modified = true;
+          continue;
+        }
 
         // Parse out the annotation row
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
@@ -852,7 +998,9 @@ public class AnnotationFile
           {
             description = line;
             if (st.hasMoreTokens())
+            {
               line = st.nextToken();
+            }
           }
 
           if (st.hasMoreTokens())
@@ -1004,8 +1152,8 @@ public class AnnotationFile
                   (StringTokenizer) _deferred_args[1], // st
                   (SequenceI) _deferred_args[2], // refSeq
                   (_deferred_args[3] == null) ? null : groupRefLookup
-                          .get((String) _deferred_args[3]) // the reference
-                                                           // group, or null
+                          .get(_deferred_args[3]) // the reference
+                                                  // group, or null
           );
         }
       }
@@ -1024,14 +1172,48 @@ public class AnnotationFile
                 (StringTokenizer) _combine_args[0], // st
                 (SequenceI) _combine_args[1], // refSeq
                 (_combine_args[2] == null) ? null : groupRefLookup
-                        .get((String) _combine_args[2]) // the reference group,
-                                                        // or null
+                        .get(_combine_args[2]) // the reference group,
+                                               // or null
         );
       }
     }
     return modified;
   }
 
+  private void parseHideCols(ColumnSelection colSel, String nextToken)
+  {
+    StringTokenizer inval = new StringTokenizer(nextToken, ",");
+    while (inval.hasMoreTokens())
+    {
+      String range = inval.nextToken().trim();
+      int from, to = range.indexOf("-");
+      if (to == -1)
+      {
+        from = to = Integer.parseInt(range);
+        if (from >= 0)
+        {
+          colSel.hideColumns(from, to);
+        }
+      }
+      else
+      {
+        from = Integer.parseInt(range.substring(0, to));
+        if (to < range.length() - 1)
+        {
+          to = Integer.parseInt(range.substring(to + 1));
+        }
+        else
+        {
+          to = from;
+        }
+        if (from > 0 && to >= from)
+        {
+          colSel.hideColumns(from, to);
+        }
+      }
+    }
+  }
+
   private Object autoAnnotsKey(AlignmentAnnotation annotation,
           SequenceI refSeq, String groupRef)
   {
@@ -1042,29 +1224,21 @@ public class AnnotationFile
 
   Annotation parseAnnotation(String string, int graphStyle)
   {
-    boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
-    // do the
-    // glyph
-    // test
-    // if we
-    // don't
-    // want
-    // secondary
-    // structure
+    // don't do the glyph test if we don't want secondary structure
+    boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH);
     String desc = null, displayChar = null;
     char ss = ' '; // secondaryStructure
     float value = 0;
     boolean parsedValue = false, dcset = false;
 
     // find colour here
-    java.awt.Color colour = null;
+    Color colour = null;
     int i = string.indexOf("[");
     int j = string.indexOf("]");
     if (i > -1 && j > -1)
     {
-      UserColourScheme ucs = new UserColourScheme();
-
-      colour = ucs.getColourFromString(string.substring(i + 1, j));
+      colour = ColorUtils.parseColourString(string.substring(i + 1,
+              j));
       if (i > 0 && string.charAt(i - 1) == ',')
       {
         // clip the preceding comma as well
@@ -1118,8 +1292,8 @@ public class AnnotationFile
         }
       }
       if (hasSymbols
-              && (token.equals("H") || token.equals("E")
-                      || token.equals("S") || token.equals(" ")))
+              && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
+                      .contains(token)))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
@@ -1166,7 +1340,7 @@ public class AnnotationFile
 
   void colourAnnotations(AlignmentI al, String label, String colour)
   {
-    UserColourScheme ucs = new UserColourScheme(colour);
+    Color awtColour = ColorUtils.parseColourString(colour);
     Annotation[] annotations;
     for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
     {
@@ -1177,7 +1351,7 @@ public class AnnotationFile
         {
           if (annotations[j] != null)
           {
-            annotations[j].colour = ucs.findColour('A');
+            annotations[j].colour = awtColour;
           }
         }
       }
@@ -1247,15 +1421,22 @@ public class AnnotationFile
           SequenceGroup groupRef)
   {
     String group = st.nextToken();
-    AlignmentAnnotation annotation = null, alannot[] = al
-            .getAlignmentAnnotation();
-    float value = new Float(st.nextToken()).floatValue();
+    AlignmentAnnotation[] alannot = al.getAlignmentAnnotation();
+    String nextToken = st.nextToken();
+    float value = 0f;
+    try
+    {
+      value = Float.valueOf(nextToken);
+    } catch (NumberFormatException e)
+    {
+      System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+              + "' invalid, setting to zero");
+    }
     String label = st.hasMoreTokens() ? st.nextToken() : null;
-    java.awt.Color colour = null;
+    Color colour = null;
     if (st.hasMoreTokens())
     {
-      UserColourScheme ucs = new UserColourScheme(st.nextToken());
-      colour = ucs.findColour('A');
+      colour = ColorUtils.parseColourString(st.nextToken());
     }
     if (alannot != null)
     {
@@ -1269,10 +1450,6 @@ public class AnnotationFile
         }
       }
     }
-    if (annotation == null)
-    {
-      return;
-    }
   }
 
   void addGroup(AlignmentI al, StringTokenizer st)
@@ -1446,7 +1623,7 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
-          sg.cs = ColourSchemeProperty.getColour(al, value);
+          sg.cs = ColourSchemeProperty.getColourScheme(al, value);
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {
@@ -1456,8 +1633,7 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("consThreshold"))
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null),
+          Conservation c = new Conservation("Group", sg.getSequences(null),
                   sg.getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
@@ -1468,7 +1644,7 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("outlineColour"))
         {
-          sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+          sg.setOutlineColour(ColorUtils.parseColourString(value));
         }
         else if (key.equalsIgnoreCase("displayBoxes"))
         {
@@ -1488,11 +1664,11 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("textCol1"))
         {
-          sg.textColour = new UserColourScheme(value).findColour('A');
+          sg.textColour = ColorUtils.parseColourString(value);
         }
         else if (key.equalsIgnoreCase("textCol2"))
         {
-          sg.textColour2 = new UserColourScheme(value).findColour('A');
+          sg.textColour2 = ColorUtils.parseColourString(value);
         }
         else if (key.equalsIgnoreCase("textColThreshold"))
         {
@@ -1500,9 +1676,8 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("idColour"))
         {
-          // consider warning if colour doesn't resolve to a real colour
-          sg.setIdColour((def = new UserColourScheme(value))
-                  .findColour('A'));
+          Color idColour = ColorUtils.parseColourString(value);
+          sg.setIdColour(idColour == null ? Color.black : idColour);
         }
         else if (key.equalsIgnoreCase("hide"))
         {
@@ -1578,6 +1753,10 @@ public class AnnotationFile
    */
   public String printCSVAnnotations(AlignmentAnnotation[] annotations)
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuffer sp = new StringBuffer();
     for (int i = 0; i < annotations.length; i++)
     {
@@ -1602,4 +1781,19 @@ public class AnnotationFile
     }
     return sp.toString();
   }
+
+  public String printAnnotationsForView(AlignViewportI viewport)
+  {
+    return printAnnotations(viewport.isShowAnnotation() ? viewport
+            .getAlignment().getAlignmentAnnotation() : null, viewport
+            .getAlignment().getGroups(), viewport.getAlignment()
+            .getProperties(), viewport.getColumnSelection(),
+            viewport.getAlignment(), null);
+  }
+
+  public String printAnnotationsForAlignment(AlignmentI al)
+  {
+    return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(),
+            al.getProperties(), null, al, null);
+  }
 }