All or nothing drawing display char

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index e4d64fa..7f6b08a 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -27,6 +27,8 @@ package jalview.datamodel;
  */\r
 public class AlignmentAnnotation\r
 {\r
+    public SequenceI sequenceRef;\r
+\r
     /** DOCUMENT ME!! */\r
     public String label;\r
 \r
@@ -36,6 +38,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */\r
     public Annotation[] annotations;\r
 \r
+    public java.util.Hashtable sequenceMapping;\r
 \r
     /** DOCUMENT ME!! */\r
     public float graphMin;\r
@@ -43,6 +46,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */\r
     public float graphMax;\r
 \r
+    public GraphLine threshold;\r
 \r
     // Graphical hints and tips\r
 \r
@@ -58,16 +62,30 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */\r
     public boolean visible = true;\r
 \r
+    public int graphGroup = -1;\r
+\r
     /** DOCUMENT ME!! */\r
     public int height = 0;\r
 \r
     public int graph = 0;\r
 \r
-    public static int NO_GRAPH = 0;\r
+    public int graphHeight = 40;\r
+\r
+    public static final int NO_GRAPH = 0;\r
 \r
-    public static int BAR_GRAPH = 1;\r
+    public static final int BAR_GRAPH = 1;\r
 \r
-    public static int LINE_GRAPH = 2;\r
+    public static final int LINE_GRAPH = 2;\r
+\r
+    public static int getGraphValueFromString(String string)\r
+    {\r
+      if(string.equalsIgnoreCase("BAR_GRAPH"))\r
+        return BAR_GRAPH;\r
+      else if(string.equalsIgnoreCase("LINE_GRAPH"))\r
+        return LINE_GRAPH;\r
+      else\r
+        return NO_GRAPH;\r
+    }\r
 \r
     /**\r
      * Creates a new AlignmentAnnotation object.\r
@@ -121,8 +139,11 @@ public class AlignmentAnnotation
         this.annotations = annotations;\r
         graph = graphType;\r
 \r
+        boolean drawValues = true;\r
+\r
         if (min == max)\r
         {\r
+            min = 999999999;\r
             for (int i = 0; i < annotations.length; i++)\r
             {\r
                 if (annotations[i] == null)\r
@@ -130,6 +151,11 @@ public class AlignmentAnnotation
                     continue;\r
                 }\r
 \r
+                if(drawValues && annotations[i].displayCharacter.length() > 1 )\r
+                {\r
+                  drawValues = false;\r
+                }\r
+\r
                 if (annotations[i].value > max)\r
                 {\r
                     max = annotations[i].value;\r
@@ -142,6 +168,15 @@ public class AlignmentAnnotation
             }\r
         }\r
 \r
+        if(!drawValues)\r
+        {\r
+          for (int i = 0; i < annotations.length; i++)\r
+          {\r
+            if (annotations[i] != null)\r
+              annotations[i].displayCharacter = "";\r
+          }\r
+        }\r
+\r
         graphMin = min;\r
         graphMax = max;\r
 \r
@@ -208,5 +243,78 @@ public class AlignmentAnnotation
         }\r
 \r
         return buffer.toString();\r
-    }\r
+      }\r
+\r
+      public void setThreshold(GraphLine line)\r
+      {\r
+        threshold = line;\r
+      }\r
+\r
+      public GraphLine getThreshold()\r
+      {\r
+          return threshold;\r
+      }\r
+\r
+      /**\r
+       * This\r
+       */\r
+      public void createSequenceMapping(SequenceI seqRef, int startRes)\r
+      {\r
+        if(seqRef == null)\r
+          return;\r
+\r
+        sequenceMapping = new java.util.Hashtable();\r
+\r
+        sequenceRef = seqRef;\r
+\r
+        if(startRes < sequenceRef.getStart())\r
+          startRes = sequenceRef.getStart();\r
+\r
+        int seqPos;\r
+\r
+        int fileOffset = 0;\r
+        if(startRes > sequenceRef.getStart())\r
+        {\r
+          fileOffset = startRes - sequenceRef.getStart();\r
+        }\r
+\r
+        for(int i = 0; i < annotations.length; i++)\r
+        {\r
+            seqPos = sequenceRef.findPosition(i + fileOffset);\r
+            if(seqPos<annotations.length)\r
+            {\r
+              if (annotations[i] != null)\r
+              {\r
+                  sequenceMapping.put(new Integer(seqPos),\r
+                                      annotations[i]);\r
+              }\r
+            }\r
+         }\r
+\r
+        adjustForAlignment();\r
+\r
+      }\r
+\r
+      public void adjustForAlignment()\r
+      {\r
+          int a=0, aSize = sequenceRef.getLength();\r
+\r
+          int position;\r
+          Annotation[] temp = new Annotation[aSize];\r
+          Integer index;\r
+          for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)\r
+          {\r
+              index = new Integer(a);\r
+              if(sequenceMapping.containsKey(index))\r
+              {\r
+                position = sequenceRef.findIndex(a)-1;\r
+\r
+                temp[position] = (Annotation)sequenceMapping.get(index);\r
+              }\r
+          }\r
+\r
+          annotations = temp;\r
+      }\r
 }\r
+\r
+\r