X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=5c5fa8f751384dcd9c890758d3b76b48ec26a7ef;hb=14985603cea28569e295ddabb219da8034f1c7b2;hp=6e121b3605294505b1e4433b740564aaadca77d6;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 6e121b3..5c5fa8f 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -27,14 +27,15 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 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;
@@ -113,14 +114,14 @@ public class AnnotationFile
 
     public HiddenSequences hidseqs;
 
-    public ColumnSelection hiddencols;
+    public HiddenColumns hiddencols;
 
     public Vector visibleGroups;
 
     public Hashtable hiddenRepSeqs;
 
     public ViewDef(String viewname, HiddenSequences hidseqs,
-            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+            HiddenColumns hiddencols, Hashtable hiddenRepSeqs)
     {
       this.viewname = viewname;
       this.hidseqs = hidseqs;
@@ -141,7 +142,8 @@ public class AnnotationFile
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
           List<SequenceGroup> list, Hashtable properties,
-          ColumnSelection cs, AlignmentI al, ViewDef view)
+ HiddenColumns cs,
+          AlignmentI al, ViewDef view)
   {
     if (view != null)
     {
@@ -170,7 +172,7 @@ public class AnnotationFile
     if (cs != null && cs.hasHiddenColumns())
     {
       text.append("VIEW_HIDECOLS\t");
-      List<int[]> hc = cs.getHiddenColumns();
+      List<int[]> hc = cs.getHiddenRegions();
       boolean comma = false;
       for (int[] r : hc)
       {
@@ -582,7 +584,7 @@ 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)
         {
@@ -664,15 +666,21 @@ public class AnnotationFile
           String file, DataSourceType protocol)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
+    HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
     if (colSel == null)
     {
       colSel = new ColumnSelection();
     }
-    boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+    if (hidden == null)
+    {
+      hidden = new HiddenColumns();
+    }
+    boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden,
             file, protocol);
-    if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+    if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
     {
       viewport.setColumnSelection(colSel);
+      viewport.getAlignment().setHiddenColumns(hidden);
     }
 
     return rslt;
@@ -684,7 +692,7 @@ public class AnnotationFile
     return readAnnotationFile(al, null, file, sourceType);
   }
 
-  public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+  public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
           String file, DataSourceType sourceType)
   {
     BufferedReader in = null;
@@ -713,7 +721,7 @@ public class AnnotationFile
       }
       if (in != null)
       {
-        return parseAnnotationFrom(al, colSel, in);
+        return parseAnnotationFrom(al, hidden, in);
       }
 
     } catch (Exception ex)
@@ -736,7 +744,7 @@ public class AnnotationFile
 
   private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
 
-  public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+  public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
           BufferedReader in) throws Exception
   {
     nlinesread = 0;
@@ -947,11 +955,11 @@ public class AnnotationFile
         {
           if (st.hasMoreTokens())
           {
-            if (colSel == null)
+            if (hidden == null)
             {
-              colSel = new ColumnSelection();
+              hidden = new HiddenColumns();
             }
-            parseHideCols(colSel, st.nextToken());
+            parseHideCols(hidden, st.nextToken());
           }
           modified = true;
           continue;
@@ -965,7 +973,7 @@ public class AnnotationFile
           }
           if (sr != null)
           {
-            if (colSel == null)
+            if (hidden == null)
             {
               System.err
                       .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
@@ -974,7 +982,7 @@ public class AnnotationFile
             else
             {
               // consider deferring this till after the file has been parsed ?
-              colSel.hideInsertionsFor(sr);
+              hidden.hideInsertionsFor(sr);
             }
           }
           modified = true;
@@ -1180,7 +1188,7 @@ public class AnnotationFile
     return modified;
   }
 
-  private void parseHideCols(ColumnSelection colSel, String nextToken)
+  private void parseHideCols(HiddenColumns hidden, String nextToken)
   {
     StringTokenizer inval = new StringTokenizer(nextToken, ",");
     while (inval.hasMoreTokens())
@@ -1192,7 +1200,7 @@ public class AnnotationFile
         from = to = Integer.parseInt(range);
         if (from >= 0)
         {
-          colSel.hideColumns(from, to);
+          hidden.hideColumns(from, to);
         }
       }
       else
@@ -1208,7 +1216,7 @@ public class AnnotationFile
         }
         if (from > 0 && to >= from)
         {
-          colSel.hideColumns(from, to);
+          hidden.hideColumns(from, to);
         }
       }
     }
@@ -1224,29 +1232,21 @@ 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
@@ -1348,7 +1348,7 @@ 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++)
     {
@@ -1359,7 +1359,7 @@ public class AnnotationFile
         {
           if (annotations[j] != null)
           {
-            annotations[j].colour = ucs.findColour('A');
+            annotations[j].colour = awtColour;
           }
         }
       }
@@ -1429,15 +1429,22 @@ 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)
     {
@@ -1451,10 +1458,6 @@ public class AnnotationFile
         }
       }
     }
-    if (annotation == null)
-    {
-      return;
-    }
   }
 
   void addGroup(AlignmentI al, StringTokenizer st)
@@ -1614,8 +1617,7 @@ 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();
@@ -1628,7 +1630,8 @@ 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"))
         {
@@ -1638,8 +1641,7 @@ 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();
@@ -1650,7 +1652,7 @@ 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"))
         {
@@ -1670,11 +1672,11 @@ 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"))
         {
@@ -1682,9 +1684,8 @@ 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"))
         {
@@ -1698,9 +1699,9 @@ public class AnnotationFile
         }
         sg.recalcConservation();
       }
-      if (sg.cs == null)
+      if (sg.getColourScheme() == null)
       {
-        sg.cs = def;
+        sg.setColourScheme(def);
       }
     }
   }
@@ -1794,7 +1795,7 @@ public class AnnotationFile
     return printAnnotations(viewport.isShowAnnotation() ? viewport
             .getAlignment().getAlignmentAnnotation() : null, viewport
             .getAlignment().getGroups(), viewport.getAlignment()
-            .getProperties(), viewport.getColumnSelection(),
+            .getProperties(), viewport.getAlignment().getHiddenColumns(),
             viewport.getAlignment(), null);
   }