X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ef903e36a6af34ad2a4e67d6bb0f9a1b6d43e440;hb=e75847be3733978d2cd51d7121778e782ad0abf3;hp=6834e7645b8bf1bcef81e0799cd01dee8bb7895d;hpb=8d6b113f475c6b5916f7685cfd289e054d95a9ee;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 6834e76..ef903e3 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.
  * 
@@ -32,9 +32,9 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 
+import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.InputStreamReader;
@@ -99,7 +99,7 @@ public class AnnotationFile
   public String printAnnotations(AlignmentAnnotation[] annotations,
           List<SequenceGroup> list, Hashtable properties)
   {
-    return printAnnotations(annotations, list, properties, null);
+    return printAnnotations(annotations, list, properties, null, null, null);
 
   }
 
@@ -109,23 +109,24 @@ public class AnnotationFile
    */
   public class ViewDef
   {
-    public String viewname;
+    // TODO this class is not used - remove?
+    public final String viewname;
 
-    public HiddenSequences hidseqs;
+    public final HiddenSequences hidseqs;
 
-    public ColumnSelection hiddencols;
+    public final ColumnSelection hiddencols;
 
-    public Vector visibleGroups;
+    // public final Vector visibleGroups;
 
-    public Hashtable hiddenRepSeqs;
+    public final Hashtable hiddenRepSeqs;
 
-    public ViewDef(String viewname, HiddenSequences hidseqs,
-            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+    public ViewDef(String vname, HiddenSequences hseqs,
+            ColumnSelection hcols, Hashtable hRepSeqs)
     {
-      this.viewname = viewname;
-      this.hidseqs = hidseqs;
-      this.hiddencols = hiddencols;
-      this.hiddenRepSeqs = hiddenRepSeqs;
+      this.viewname = vname;
+      this.hidseqs = hseqs;
+      this.hiddencols = hcols;
+      this.hiddenRepSeqs = hRepSeqs;
     }
   }
 
@@ -140,16 +141,56 @@ 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 (views != null)
+    if (view != null)
     {
-      // are views defined and then annotation added to alignment or the other
-      // way around ?
-
+      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;
@@ -201,7 +242,7 @@ 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
@@ -254,8 +295,7 @@ 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);
             }
           }
@@ -291,13 +331,13 @@ 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 = ",";
@@ -432,7 +472,9 @@ 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();
@@ -495,7 +537,7 @@ public class AnnotationFile
     return false;
   }
 
-  public void printGroups(List<SequenceGroup> list)
+  protected void printGroups(List<SequenceGroup> list)
   {
     SequenceI seqrep = null;
     for (SequenceGroup sg : list)
@@ -541,7 +583,8 @@ public class AnnotationFile
       if (sg.cs != null)
       {
         text.append("colour=");
-        text.append(ColourSchemeProperty.getColourName(sg.cs));
+        text.append(ColourSchemeProperty.getColourName(sg.cs
+                .getColourScheme()));
         text.append("\t");
         if (sg.cs.getThreshold() != 0)
         {
@@ -620,7 +663,7 @@ public class AnnotationFile
   String refSeqId = null;
 
   public boolean annotateAlignmentView(AlignViewportI viewport,
-          String file, String protocol)
+          String file, DataSourceType protocol)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel == null)
@@ -629,40 +672,40 @@ public class AnnotationFile
     }
     boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
             file, protocol);
-    if (rslt
-            && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+    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, protocol);
+    return readAnnotationFile(al, null, file, sourceType);
   }
 
   public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
-          String file, String protocol)
+          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)
@@ -696,8 +739,7 @@ public class AnnotationFile
   private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
 
   public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
-          BufferedReader in)
-          throws Exception
+          BufferedReader in) throws Exception
   {
     nlinesread = 0;
     ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
@@ -790,8 +832,8 @@ 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;
         }
@@ -804,8 +846,8 @@ 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;
         }
@@ -888,6 +930,12 @@ 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)
@@ -897,6 +945,19 @@ public class AnnotationFile
           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;
@@ -1094,7 +1155,7 @@ public class AnnotationFile
                   (SequenceI) _deferred_args[2], // refSeq
                   (_deferred_args[3] == null) ? null : groupRefLookup
                           .get(_deferred_args[3]) // the reference
-                                                           // group, or null
+                                                  // group, or null
           );
         }
       }
@@ -1114,13 +1175,47 @@ public class AnnotationFile
                 (SequenceI) _combine_args[1], // refSeq
                 (_combine_args[2] == null) ? null : groupRefLookup
                         .get(_combine_args[2]) // the reference group,
-                                                        // or null
+                                               // 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)
   {
@@ -1131,29 +1226,21 @@ 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
@@ -1207,8 +1294,8 @@ 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
@@ -1255,7 +1342,7 @@ 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++)
     {
@@ -1266,7 +1353,7 @@ public class AnnotationFile
         {
           if (annotations[j] != null)
           {
-            annotations[j].colour = ucs.findColour('A');
+            annotations[j].colour = awtColour;
           }
         }
       }
@@ -1336,15 +1423,22 @@ 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)
     {
@@ -1358,10 +1452,6 @@ public class AnnotationFile
         }
       }
     }
-    if (annotation == null)
-    {
-      return;
-    }
   }
 
   void addGroup(AlignmentI al, StringTokenizer st)
@@ -1521,8 +1611,7 @@ public class AnnotationFile
     if (sg != null)
     {
       String keyValue, key, value;
-      ColourSchemeI def = sg.cs;
-      sg.cs = null;
+      ColourSchemeI def = sg.getColourScheme();
       while (st.hasMoreTokens())
       {
         keyValue = st.nextToken();
@@ -1535,7 +1624,8 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
-          sg.cs = ColourSchemeProperty.getColour(al, value);
+          sg.cs.setColourScheme(ColourSchemeProperty
+                  .getColourScheme(al, value));
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {
@@ -1545,8 +1635,7 @@ 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();
@@ -1557,7 +1646,7 @@ 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"))
         {
@@ -1577,11 +1666,11 @@ 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"))
         {
@@ -1589,9 +1678,8 @@ 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"))
         {
@@ -1605,9 +1693,9 @@ public class AnnotationFile
         }
         sg.recalcConservation();
       }
-      if (sg.cs == null)
+      if (sg.getColourScheme() == null)
       {
-        sg.cs = def;
+        sg.setColourScheme(def);
       }
     }
   }
@@ -1667,6 +1755,10 @@ public class AnnotationFile
    */
   public String printCSVAnnotations(AlignmentAnnotation[] annotations)
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuffer sp = new StringBuffer();
     for (int i = 0; i < annotations.length; i++)
     {
@@ -1697,12 +1789,13 @@ public class AnnotationFile
     return printAnnotations(viewport.isShowAnnotation() ? viewport
             .getAlignment().getAlignmentAnnotation() : null, viewport
             .getAlignment().getGroups(), viewport.getAlignment()
-            .getProperties());
+            .getProperties(), viewport.getColumnSelection(),
+            viewport.getAlignment(), null);
   }
 
   public String printAnnotationsForAlignment(AlignmentI al)
   {
     return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(),
-            al.getProperties());
+            al.getProperties(), null, al, null);
   }
 }