Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 34fdabe..9a4071d 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -32,8 +32,9 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 
+import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.InputStreamReader;
@@ -581,7 +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)
         {
@@ -660,7 +661,7 @@ 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)
@@ -678,31 +679,31 @@ public class AnnotationFile
   }
 
   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)
@@ -1223,29 +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
@@ -1347,7 +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++)
     {
@@ -1358,7 +1351,7 @@ public class AnnotationFile
         {
           if (annotations[j] != null)
           {
-            annotations[j].colour = ucs.findColour('A');
+            annotations[j].colour = awtColour;
           }
         }
       }
@@ -1428,15 +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)
     {
@@ -1450,10 +1450,6 @@ public class AnnotationFile
         }
       }
     }
-    if (annotation == null)
-    {
-      return;
-    }
   }
 
   void addGroup(AlignmentI al, StringTokenizer st)
@@ -1613,8 +1609,7 @@ 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();
@@ -1627,7 +1622,8 @@ 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"))
         {
@@ -1637,9 +1633,8 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("consThreshold"))
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
-          Conservation c = new Conservation("Group", 3,
-                  sg.getSequences(null), sg.getStartRes(),
-                  sg.getEndRes() + 1);
+          Conservation c = new Conservation("Group", sg.getSequences(null),
+                  sg.getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25); // TODO: refer to conservation percent threshold
@@ -1649,7 +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"))
         {
@@ -1669,11 +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"))
         {
@@ -1681,9 +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"))
         {
@@ -1697,9 +1691,9 @@ public class AnnotationFile
         }
         sg.recalcConservation();
       }
-      if (sg.cs == null)
+      if (sg.getColourScheme() == null)
       {
-        sg.cs = def;
+        sg.setColourScheme(def);
       }
     }
   }