JAL-2231 save preferred scroll height _without_ progress bar message

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 33c7ff3..7d8f1bf 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -717,6 +717,7 @@ public class StructureChooser extends GStructureChooser implements
   {
     final long progressSessionId = System.currentTimeMillis();
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+    final int preferredHeight = pnl_filter.getHeight();
     ssm.setProgressIndicator(this);
     ssm.setProgressSessionId(progressSessionId);
     new Thread(new Runnable()
@@ -724,84 +725,82 @@ public class StructureChooser extends GStructureChooser implements
       @Override
       public void run()
       {
-    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
-            .getSelectedItem());
-    String currentView = selectedFilterOpt.getView();
-    if (currentView == VIEWS_FILTER)
-    {
+        FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+                .getSelectedItem());
+        String currentView = selectedFilterOpt.getView();
+        if (currentView == VIEWS_FILTER)
+        {
           int pdbIdColIndex = getResultTable().getColumn("PDB Id")
                   .getModelIndex();
           int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
-              .getModelIndex();
+                  .getModelIndex();
           int[] selectedRows = getResultTable().getSelectedRows();
-      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
-      int count = 0;
-      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
-      for (int row : selectedRows)
-      {
+          PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+          int count = 0;
+          ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+          for (int row : selectedRows)
+          {
             String pdbIdStr = getResultTable().getValueAt(row,
-                    pdbIdColIndex)
-                .toString();
+                    pdbIdColIndex).toString();
             SequenceI selectedSeq = (SequenceI) getResultTable()
-                    .getValueAt(row,
-                refSeqColIndex);
-        selectedSeqsToView.add(selectedSeq);
+                    .getValueAt(row, refSeqColIndex);
+            selectedSeqsToView.add(selectedSeq);
             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
             if (pdbEntry == null)
             {
               pdbEntry = getFindEntry(pdbIdStr,
                       selectedSeq.getAllPDBEntries());
             }
-        if (pdbEntry == null)
-        {
-          pdbEntry = new PDBEntry();
-          pdbEntry.setId(pdbIdStr);
-          pdbEntry.setType(PDBEntry.Type.PDB);
-          selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
-        }
-        pdbEntriesToView[count++] = pdbEntry;
-      }
-      SequenceI[] selectedSeqs = selectedSeqsToView
-              .toArray(new SequenceI[selectedSeqsToView.size()]);
+            if (pdbEntry == null)
+            {
+              pdbEntry = new PDBEntry();
+              pdbEntry.setId(pdbIdStr);
+              pdbEntry.setType(PDBEntry.Type.PDB);
+              selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
+            }
+            pdbEntriesToView[count++] = pdbEntry;
+          }
+          SequenceI[] selectedSeqs = selectedSeqsToView
+                  .toArray(new SequenceI[selectedSeqsToView.size()]);
           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
-    }
-    else if (currentView == VIEWS_LOCAL_PDB)
-    {
-      int[] selectedRows = tbl_local_pdb.getSelectedRows();
-      PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
-      int count = 0;
+        }
+        else if (currentView == VIEWS_LOCAL_PDB)
+        {
+          int[] selectedRows = tbl_local_pdb.getSelectedRows();
+          PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+          int count = 0;
           int pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
                   .getModelIndex();
-      int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
-              .getModelIndex();
-      ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
-      for (int row : selectedRows)
-      {
-        PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
-                pdbIdColIndex);
-        pdbEntriesToView[count++] = pdbEntry;
-        SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
-                refSeqColIndex);
-        selectedSeqsToView.add(selectedSeq);
-      }
-      SequenceI[] selectedSeqs = selectedSeqsToView
-              .toArray(new SequenceI[selectedSeqsToView.size()]);
+          int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+                  .getModelIndex();
+          ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+          for (int row : selectedRows)
+          {
+            PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+                    pdbIdColIndex);
+            pdbEntriesToView[count++] = pdbEntry;
+            SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(
+                    row, refSeqColIndex);
+            selectedSeqsToView.add(selectedSeq);
+          }
+          SequenceI[] selectedSeqs = selectedSeqsToView
+                  .toArray(new SequenceI[selectedSeqsToView.size()]);
           launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
-    }
-    else if (currentView == VIEWS_ENTER_ID)
-    {
-      SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
-              .getCmb_assSeq().getSelectedItem()).getSequence();
-      if (userSelectedSeq != null)
-      {
-        selectedSequence = userSelectedSeq;
-      }
+        }
+        else if (currentView == VIEWS_ENTER_ID)
+        {
+          SequenceI userSelectedSeq = ((AssociateSeqOptions) idInputAssSeqPanel
+                  .getCmb_assSeq().getSelectedItem()).getSequence();
+          if (userSelectedSeq != null)
+          {
+            selectedSequence = userSelectedSeq;
+          }
 
-      String pdbIdStr = txt_search.getText();
-      PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
-      if (pdbEntry == null)
-      {
-        pdbEntry = new PDBEntry();
+          String pdbIdStr = txt_search.getText();
+          PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
+          if (pdbEntry == null)
+          {
+            pdbEntry = new PDBEntry();
             if (pdbIdStr.split(":").length > 1)
             {
               pdbEntry.setId(pdbIdStr.split(":")[0]);
@@ -811,31 +810,31 @@ public class StructureChooser extends GStructureChooser implements
             {
               pdbEntry.setId(pdbIdStr);
             }
-        pdbEntry.setType(PDBEntry.Type.PDB);
-        selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
-      }
+            pdbEntry.setType(PDBEntry.Type.PDB);
+            selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+          }
 
-      PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
+          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,
+                          jalview.io.AppletFormatAdapter.FILE,
+                          selectedSequence, true, Desktop.instance);
 
           launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
                   new SequenceI[] { selectedSequence });
-    }
-        closeAction();
+        }
+        closeAction(preferredHeight);
       }
     }).start();
   }
@@ -865,7 +864,7 @@ public class StructureChooser extends GStructureChooser implements
 
     if (SiftsSettings.isMapWithSifts())
     {
-      ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+      List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
       int p = 0;
       // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
       // real PDB ID. For moment, we can also safely do this if there is already
@@ -906,7 +905,8 @@ public class StructureChooser extends GStructureChooser implements
         {
           seqWithoutSrcDBRef[x++] = fSeq;
         }
-        new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+        DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+        dbRefFetcher.fetchDBRefs(true);
       }
     }
     if (pdbEntriesToView.length > 1)