X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=7e6b904e28f75530d00d6fd6fd6bf6c5869aac1b;hb=refs%2Fheads%2Fspike%2FJAL-4047%2FJAL-4048_columns_in_sequenceID;hp=0f418508abdd229bde007483606a24e5b448a996;hpb=0ae965fc73680bdc69b06986c060ff17342c4787;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0f41850..7e6b904 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -34,6 +34,7 @@ import java.util.Map.Entry;
 import jalview.analysis.Rna;
 import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.analysis.WUSSParseException;
+import jalview.structure.StructureImportSettings;
 
 /**
  * DOCUMENT ME!
@@ -43,6 +44,7 @@ import jalview.analysis.WUSSParseException;
  */
 public class AlignmentAnnotation
 {
+
   private static final String ANNOTATION_ID_PREFIX = "ann";
 
   /*
@@ -96,6 +98,21 @@ public class AlignmentAnnotation
   private long invalidrnastruc = -2;
 
   /**
+   * the type of temperature factor plot (if it is one)
+   */
+  private StructureImportSettings.TFType tfType = StructureImportSettings.TFType.DEFAULT;
+
+  public void setTFType(StructureImportSettings.TFType t)
+  {
+    tfType = t;
+  }
+
+  public StructureImportSettings.TFType getTFType()
+  {
+    return tfType;
+  }
+
+  /**
    * Updates the _rnasecstr field Determines the positions that base pair and
    * the positions of helices based on secondary structure from a Stockholm file
    * 
@@ -109,7 +126,7 @@ public class AlignmentAnnotation
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
-      // DEBUG System.out.println(px);
+      // DEBUG jalview.bin.Console.outPrintln(px);
       invalidrnastruc = px.getProblemPos();
     }
     if (invalidrnastruc > -1)
@@ -125,7 +142,7 @@ public class AlignmentAnnotation
       scaleColLabel = true;
       _markRnaHelices();
     }
-    // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+    // jalview.bin.Console.outPrintln("featuregroup " + _rnasecstr[0].getFeatureGroup());
 
   }
 
@@ -139,10 +156,10 @@ public class AlignmentAnnotation
     {
 
       /*
-       * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+       * jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
        * this.annotation._rnasecstr[x].getBegin());
        */
-      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+      // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
       int val = 0;
       try
       {
@@ -289,6 +306,13 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
+  public static final int CONTACT_MAP = 4;
+
+  /**
+   * property that when set to non-empty string disables display of column groups defined on the contact matrix
+   */
+  public static final String CONTACT_MAP_NOGROUPS = "CMNOGRPS";
+
   public boolean belowAlignment = true;
 
   public SequenceGroup groupRef = null;
@@ -362,7 +386,7 @@ public class AlignmentAnnotation
     char firstChar = 0;
     for (int i = 0; i < annotations.length; i++)
     {
-      // DEBUG System.out.println(i + ": " + annotations[i]);
+      // DEBUG jalview.bin.Console.outPrintln(i + ": " + annotations[i]);
       if (annotations[i] == null)
       {
         continue;
@@ -370,14 +394,14 @@ public class AlignmentAnnotation
       if (annotations[i].secondaryStructure == 'H'
               || annotations[i].secondaryStructure == 'E')
       {
-        // DEBUG System.out.println( "/H|E/ '" +
+        // DEBUG jalview.bin.Console.outPrintln( "/H|E/ '" +
         // annotations[i].secondaryStructure + "'");
         hasIcons |= true;
       }
       else
       // Check for RNA secondary structure
       {
-        // DEBUG System.out.println( "/else/ '" +
+        // DEBUG jalview.bin.Console.outPrintln( "/else/ '" +
         // annotations[i].secondaryStructure + "'");
         // TODO: 2.8.2 should this ss symbol validation check be a function in
         // RNA/ResidueProperties ?
@@ -422,7 +446,7 @@ public class AlignmentAnnotation
         }
       }
 
-      // System.out.println("displaychar " + annotations[i].displayCharacter);
+      // jalview.bin.Console.outPrintln("displaychar " + annotations[i].displayCharacter);
 
       if (annotations[i].displayCharacter == null
               || annotations[i].displayCharacter.length() == 0)
@@ -549,12 +573,12 @@ public class AlignmentAnnotation
                       : annotations[index + offset].displayCharacter == null
                               || annotations[index
                                       + offset].displayCharacter
-                                      .length() == 0
-                                              ? annotations[index
-                                                      + offset].secondaryStructure
-                                              : annotations[index
-                                                      + offset].displayCharacter
-                                                      .charAt(0));
+                                              .length() == 0
+                                                      ? annotations[index
+                                                              + offset].secondaryStructure
+                                                      : annotations[index
+                                                              + offset].displayCharacter
+                                                                      .charAt(0));
     }
 
     @Override
@@ -807,6 +831,7 @@ public class AlignmentAnnotation
       {
         this.sequenceMapping = null;
       }
+
     }
     // TODO: check if we need to do this: JAL-952
     // if (this.isrna=annotation.isrna)
@@ -1725,5 +1750,23 @@ public class AlignmentAnnotation
     }
     return aa;
   }
+  
+  /**
+   * convenience method to check for the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+   * @return true if no CONTACT_MAP_NOGROUPS property is found, or it is set to ""
+   */
+  public boolean isShowGroupsForContactMatrix()
+  {
+    return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS)==null || "".equals(getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS));
+  }
+  /**
+   * set the 'CONTACT_MAP_NOGROUPS' property for this alignment annotation row
+   * @see isShowGroupsForContactMatrix
+   */
+  public void setShowGroupsForContactMatrix(boolean showGroups)
+  {
+    setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS, showGroups ? "" : "nogroups");
+  }
+
 
 }