JAL-1551 spotlessApply

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 5708f01..b5987f4 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,10 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -31,9 +27,15 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+import jalview.structure.StructureImportSettings;
+
 /**
  * DOCUMENT ME!
  * 
@@ -42,6 +44,7 @@ import java.util.Map.Entry;
  */
 public class AlignmentAnnotation
 {
+
   private static final String ANNOTATION_ID_PREFIX = "ann";
 
   /*
@@ -95,6 +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
    * 
@@ -181,7 +199,8 @@ public class AlignmentAnnotation
     return rnaSecondaryStructureEquivalent(that, true);
   }
 
-  public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
+  public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that,
+          boolean compareType)
   {
     SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
     SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
@@ -194,21 +213,28 @@ public class AlignmentAnnotation
       return false;
     }
     Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
-                                                   // like this
+                                                 // like this
     Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
-                                                   // like this
-    for (int i=0; i < thisSfArray.length; i++) {
+                                                 // like this
+    for (int i = 0; i < thisSfArray.length; i++)
+    {
       SequenceFeature thisSf = thisSfArray[i];
       SequenceFeature thatSf = thatSfArray[i];
-      if (compareType) {
-        if (thisSf.getType() == null || thatSf.getType() == null) {
-          if (thisSf.getType() == null && thatSf.getType() == null) {
+      if (compareType)
+      {
+        if (thisSf.getType() == null || thatSf.getType() == null)
+        {
+          if (thisSf.getType() == null && thatSf.getType() == null)
+          {
             continue;
-          } else {
+          }
+          else
+          {
             return false;
           }
         }
-        if (! thisSf.getType().equals(thatSf.getType())) {
+        if (!thisSf.getType().equals(thatSf.getType()))
+        {
           return false;
         }
       }
@@ -280,7 +306,7 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
-  public static final int CUSTOMRENDERER = 4;
+  public static final int CONTACT_MAP = 4;
 
   public boolean belowAlignment = true;
 
@@ -374,21 +400,24 @@ public class AlignmentAnnotation
         // annotations[i].secondaryStructure + "'");
         // TODO: 2.8.2 should this ss symbol validation check be a function in
         // RNA/ResidueProperties ?
+        // allow for DSSP extended code:
+        // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code
+        // GHITEBS as well as C and X (for missing?)
         if (annotations[i].secondaryStructure == '('
                 || annotations[i].secondaryStructure == '['
                 || annotations[i].secondaryStructure == '<'
                 || annotations[i].secondaryStructure == '{'
                 || annotations[i].secondaryStructure == 'A'
-                || annotations[i].secondaryStructure == 'B'
-                || annotations[i].secondaryStructure == 'C'
+                // || annotations[i].secondaryStructure == 'B'
+                // || annotations[i].secondaryStructure == 'C'
                 || annotations[i].secondaryStructure == 'D'
                 // || annotations[i].secondaryStructure == 'E' // ambiguous on
                 // its own -- already checked above
                 || annotations[i].secondaryStructure == 'F'
-                || annotations[i].secondaryStructure == 'G'
+                // || annotations[i].secondaryStructure == 'G'
                 // || annotations[i].secondaryStructure == 'H' // ambiguous on
                 // its own -- already checked above
-                || annotations[i].secondaryStructure == 'I'
+                // || annotations[i].secondaryStructure == 'I'
                 || annotations[i].secondaryStructure == 'J'
                 || annotations[i].secondaryStructure == 'K'
                 || annotations[i].secondaryStructure == 'L'
@@ -398,12 +427,12 @@ public class AlignmentAnnotation
                 || annotations[i].secondaryStructure == 'P'
                 || annotations[i].secondaryStructure == 'Q'
                 || annotations[i].secondaryStructure == 'R'
-                || annotations[i].secondaryStructure == 'S'
-                || annotations[i].secondaryStructure == 'T'
+                // || annotations[i].secondaryStructure == 'S'
+                // || annotations[i].secondaryStructure == 'T'
                 || annotations[i].secondaryStructure == 'U'
                 || annotations[i].secondaryStructure == 'V'
                 || annotations[i].secondaryStructure == 'W'
-                || annotations[i].secondaryStructure == 'X'
+                // || annotations[i].secondaryStructure == 'X'
                 || annotations[i].secondaryStructure == 'Y'
                 || annotations[i].secondaryStructure == 'Z')
         {
@@ -797,6 +826,7 @@ public class AlignmentAnnotation
       {
         this.sequenceMapping = null;
       }
+
     }
     // TODO: check if we need to do this: JAL-952
     // if (this.isrna=annotation.isrna)
@@ -1227,7 +1257,7 @@ public class AlignmentAnnotation
   {
     if (seqname && this.sequenceRef != null)
     {
-      int i = description.toLowerCase().indexOf("<html>");
+      int i = description.toLowerCase(Locale.ROOT).indexOf("<html>");
       if (i > -1)
       {
         // move the html tag to before the sequence reference.