Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 21b6e4f..c6ba8e9 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -32,6 +32,7 @@ import jalview.fts.api.FTSRestClientI;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
 import jalview.jbgui.GStructureChooser;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
@@ -65,6 +66,8 @@ import javax.swing.table.AbstractTableModel;
 public class StructureChooser extends GStructureChooser implements
         IProgressIndicator
 {
+  private static int MAX_QLENGTH = 7820;
+
   private SequenceI selectedSequence;
 
   private SequenceI[] selectedSequences;
@@ -83,8 +86,6 @@ public class StructureChooser extends GStructureChooser implements
 
   private boolean cachedPDBExists;
 
-  private static int MAX_QLENGHT = 7820;
-
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
@@ -262,7 +263,7 @@ public class StructureChooser extends GStructureChooser implements
     Set<String> seqRefs = new LinkedHashSet<String>();
 
     if (seq.getAllPDBEntries() != null
-            && queryBuilder.length() < MAX_QLENGHT)
+            && queryBuilder.length() < MAX_QLENGTH)
     {
       for (PDBEntry entry : seq.getAllPDBEntries())
       {
@@ -280,7 +281,7 @@ public class StructureChooser extends GStructureChooser implements
       for (DBRefEntry dbRef : seq.getDBRefs())
       {
         if (isValidSeqName(getDBRefId(dbRef))
-                && queryBuilder.length() < MAX_QLENGHT)
+                && queryBuilder.length() < MAX_QLENGTH)
         {
           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
           {
@@ -755,7 +756,7 @@ public class StructureChooser extends GStructureChooser implements
           int[] selectedRows = getResultTable().getSelectedRows();
           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
           int count = 0;
-          ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+          List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
           for (int row : selectedRows)
           {
             String pdbIdStr = getResultTable().getValueAt(row,
@@ -791,7 +792,7 @@ public class StructureChooser extends GStructureChooser implements
                   .getModelIndex();
           int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
                   .getModelIndex();
-          ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+          List<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
           for (int row : selectedRows)
           {
             PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
@@ -835,19 +836,19 @@ public class StructureChooser extends GStructureChooser implements
           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
           launchStructureViewer(ssm, pdbEntriesToView, ap,
                   new SequenceI[] { selectedSequence });
-        }
-        else if (currentView == VIEWS_FROM_FILE)
-        {
-          SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
-                  .getCmb_assSeq().getSelectedItem()).getSequence();
-          if (userSelectedSeq != null)
-          {
-            selectedSequence = userSelectedSeq;
-          }
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(selectedPdbFileName,
-                          jalview.io.AppletFormatAdapter.FILE,
-                          selectedSequence, true, Desktop.instance);
+    }
+    else if (currentView == VIEWS_FROM_FILE)
+    {
+      SequenceI userSelectedSeq = ((AssociateSeqOptions) fileChooserAssSeqPanel
+              .getCmb_assSeq().getSelectedItem()).getSequence();
+      if (userSelectedSeq != null)
+      {
+        selectedSequence = userSelectedSeq;
+      }
+      PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+              .associatePdbWithSeq(selectedPdbFileName,
+                          DataSourceType.FILE,
+                      selectedSequence, true, Desktop.instance);
 
           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
                   new SequenceI[] { selectedSequence });