X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=09859c9aff81aaae02736c58a449cbd7ba4166ef;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=2182b24b9b7bb6154102bf0cdbf3b0582f47cf1f;hpb=c424c88d659c131acbcc917fc34d89bff46f7b15;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2182b24..09859c9 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -25,6 +25,7 @@ import java.io.BufferedReader;
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -1549,110 +1550,120 @@ public class AnnotationFile
     }
 
     String name = st.nextToken();
-    SequenceGroup sg = null;
-    for (SequenceGroup _sg : al.getGroups())
+
+    Map<String, String> properties = new HashMap<>();
+    while (st.hasMoreTokens())
     {
-      if ((sg = _sg).getName().equals(name))
-      {
-        break;
-      }
-      else
+      String keyValue = st.nextToken();
+      String key = keyValue.substring(0, keyValue.indexOf("="));
+      String value = keyValue.substring(keyValue.indexOf("=") + 1);
+      properties.put(key, value);
+    }
+
+    for (SequenceGroup sg : al.getGroups())
+    {
+      if (sg.getName().equals(name))
       {
-        sg = null;
+        addProperties(sg, properties, al);
       }
     }
+  }
 
-    if (sg != null)
+  /**
+   * Helper method that applies any specified properties to a SequenceGroup
+   * 
+   * @param sg
+   * @param properties
+   * @param al
+   */
+  private void addProperties(SequenceGroup sg,
+          Map<String, String> properties, AlignmentI al)
+  {
+    ColourSchemeI def = sg.getColourScheme();
+    for (String key : properties.keySet())
     {
-      String keyValue, key, value;
-      ColourSchemeI def = sg.getColourScheme();
-      while (st.hasMoreTokens())
+      String value = properties.get(key);
+      if (key.equalsIgnoreCase("description"))
       {
-        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"))
-        {
-          // TODO need to notify colourscheme of view reference once it is
-          // available
-          sg.cs.setColourScheme(
-                  ColourSchemeProperty.getColourScheme(null, al, value));
-        }
-        else if (key.equalsIgnoreCase("pidThreshold"))
-        {
-          sg.cs.setThreshold(Integer.parseInt(value), true);
+        sg.setDescription(value);
+      }
+      else if (key.equalsIgnoreCase("colour"))
+      {
+        // TODO need to notify colourscheme of view reference once it is
+        // available
+        sg.cs.setColourScheme(
+                ColourSchemeProperty.getColourScheme(null, 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", sg.getSequences(null),
-                  sg.getStartRes(), sg.getEndRes() + 1);
+      }
+      else if (key.equalsIgnoreCase("consThreshold"))
+      {
+        sg.cs.setConservationInc(Integer.parseInt(value));
+        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
+        c.calculate();
+        c.verdict(false, 25); // TODO: refer to conservation percent threshold
 
-          sg.cs.setConservation(c);
+        sg.cs.setConservation(c);
 
-        }
-        else if (key.equalsIgnoreCase("outlineColour"))
-        {
-          sg.setOutlineColour(ColorUtils.parseColourString(value));
-        }
-        else if (key.equalsIgnoreCase("displayBoxes"))
-        {
-          sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
-        }
-        else if (key.equalsIgnoreCase("showUnconserved"))
-        {
-          sg.setShowNonconserved(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 = ColorUtils.parseColourString(value);
-        }
-        else if (key.equalsIgnoreCase("textCol2"))
-        {
-          sg.textColour2 = ColorUtils.parseColourString(value);
-        }
-        else if (key.equalsIgnoreCase("textColThreshold"))
-        {
-          sg.thresholdTextColour = Integer.parseInt(value);
-        }
-        else if (key.equalsIgnoreCase("idColour"))
-        {
-          Color idColour = ColorUtils.parseColourString(value);
-          sg.setIdColour(idColour == null ? Color.black : idColour);
-        }
-        else if (key.equalsIgnoreCase("hide"))
-        {
-          // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
-          sg.setHidereps(true);
-        }
-        else if (key.equalsIgnoreCase("hidecols"))
-        {
-          // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
-          sg.setHideCols(true);
-        }
-        sg.recalcConservation();
       }
-      if (sg.getColourScheme() == null)
+      else if (key.equalsIgnoreCase("outlineColour"))
       {
-        sg.setColourScheme(def);
+        sg.setOutlineColour(ColorUtils.parseColourString(value));
       }
+      else if (key.equalsIgnoreCase("displayBoxes"))
+      {
+        sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
+      }
+      else if (key.equalsIgnoreCase("showUnconserved"))
+      {
+        sg.setShowNonconserved(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 = ColorUtils.parseColourString(value);
+      }
+      else if (key.equalsIgnoreCase("textCol2"))
+      {
+        sg.textColour2 = ColorUtils.parseColourString(value);
+      }
+      else if (key.equalsIgnoreCase("textColThreshold"))
+      {
+        sg.thresholdTextColour = Integer.parseInt(value);
+      }
+      else if (key.equalsIgnoreCase("idColour"))
+      {
+        Color idColour = ColorUtils.parseColourString(value);
+        sg.setIdColour(idColour == null ? Color.black : idColour);
+      }
+      else if (key.equalsIgnoreCase("hide"))
+      {
+        // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
+        sg.setHidereps(true);
+      }
+      else if (key.equalsIgnoreCase("hidecols"))
+      {
+        // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
+        sg.setHideCols(true);
+      }
+      sg.recalcConservation();
+    }
+
+    if (sg.getColourScheme() == null)
+    {
+      sg.setColourScheme(def);
     }
   }