JAL-1551 spotlessApply

[jalview.git] / src / jalview / ws / datamodel / alphafold / PAEContactMatrix.java

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 0ba9584..b29c0d5 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -35,7 +35,8 @@ import jalview.util.MapList;
 import jalview.util.MapUtils;
 import jalview.ws.dbsources.EBIAlfaFold;
 
-public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
+public class PAEContactMatrix extends
+        MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
 {
   int maxrow = 0, maxcol = 0;
 
@@ -43,9 +44,9 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
 
   float maxscore;
 
-
   @SuppressWarnings("unchecked")
-  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws FileFormatException
+  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+          throws FileFormatException
   {
     setRefSeq(_refSeq);
     // convert the lists to primitive arrays and store
@@ -93,17 +94,18 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
 
   /**
    * new matrix with specific mapping to a reference sequence
+   * 
    * @param newRefSeq
    * @param newFromMapList
    * @param elements2
-   * @param grps2 
+   * @param grps2
    */
-  public PAEContactMatrix(SequenceI newRefSeq,
-          MapList newFromMapList, float[][] elements2, GroupSet grps2)
+  public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList,
+          float[][] elements2, GroupSet grps2)
   {
-    this(newRefSeq,elements2);
+    this(newRefSeq, elements2);
     toSeq = newFromMapList;
-    grps= grps2;
+    grps = grps2;
   }
 
   /**
@@ -144,7 +146,7 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
         {
           elements[row][col++] = (float) ((Long) d).longValue();
         }
-        
+
         if (maxscore < elements[row][col - 1])
         {
           maxscore = elements[row][col - 1];
@@ -213,20 +215,20 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   @Override
   public ContactListI getContactList(final int column)
   {
-//    final int _column;
-//    if (toSeq != null)
-//    {
-//      int[] word = toSeq.locateInTo(column, column);
-//      if (word == null)
-//      {
-//        return null;
-//      }
-//      _column = word[0];
-//    }
-//    else
-//    {
-//      _column = column;
-//    }
+    // final int _column;
+    // if (toSeq != null)
+    // {
+    // int[] word = toSeq.locateInTo(column, column);
+    // if (word == null)
+    // {
+    // return null;
+    // }
+    // _column = word[0];
+    // }
+    // else
+    // {
+    // _column = column;
+    // }
     if (column < 0 || column >= elements.length)
     {
       return null;
@@ -263,6 +265,7 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   {
     return elements[_column][i];
   }
+
   @Override
   public float getMin()
   {
@@ -278,17 +281,18 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   @Override
   public String getAnnotDescr()
   {
-    return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName()));
+    return "Predicted Alignment Error"
+            + ((refSeq == null) ? "" : (" for " + refSeq.getName()));
   }
 
   @Override
   public String getAnnotLabel()
   {
     StringBuilder label = new StringBuilder("PAE Matrix");
-    //if (this.getReferenceSeq() != null)
-    //{
-    //  label.append(":").append(this.getReferenceSeq().getDisplayId(false));
-    //}
+    // if (this.getReferenceSeq() != null)
+    // {
+    // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+    // }
     return label.toString();
   }
 
@@ -311,39 +315,44 @@ public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> im
   {
     return length;
   }
-  
-  public static void validateContactMatrixFile(String fileName) throws FileFormatException,IOException
+
+  public static void validateContactMatrixFile(String fileName)
+          throws FileFormatException, IOException
   {
-    FileInputStream infile=null;
-    try {
+    FileInputStream infile = null;
+    try
+    {
       infile = new FileInputStream(new File(fileName));
     } catch (Throwable t)
     {
-      new IOException("Couldn't open "+fileName,t);      
+      new IOException("Couldn't open " + fileName, t);
     }
-    
-    
-    JSONObject paeDict=null;
-    try {
+
+    JSONObject paeDict = null;
+    try
+    {
       paeDict = EBIAlfaFold.parseJSONtoPAEContactMatrix(infile);
     } catch (Throwable t)
     {
-      new FileFormatException("Couldn't parse "+fileName+" as a JSON dict or array containing a dict");
+      new FileFormatException("Couldn't parse " + fileName
+              + " as a JSON dict or array containing a dict");
     }
-    
-    PAEContactMatrix matrix = new PAEContactMatrix(new SequenceDummy("Predicted"), (Map<String,Object>)paeDict);
-    if (matrix.getWidth()<=0)
+
+    PAEContactMatrix matrix = new PAEContactMatrix(
+            new SequenceDummy("Predicted"), (Map<String, Object>) paeDict);
+    if (matrix.getWidth() <= 0)
     {
-      throw new FileFormatException("No data in PAE matrix read from '"+fileName+"'");
+      throw new FileFormatException(
+              "No data in PAE matrix read from '" + fileName + "'");
     }
   }
 
   @Override
-  protected PAEContactMatrix newMappableContactMatrix(
-          SequenceI newRefSeq, MapList newFromMapList)
+  protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq,
+          MapList newFromMapList)
   {
-    PAEContactMatrix pae=new PAEContactMatrix(newRefSeq, newFromMapList,
-              elements, new GroupSet(grps));
+    PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList,
+            elements, new GroupSet(grps));
     return pae;
-  } 
+  }
 }