JAL-2386 simplify changeColour (doesn't change colour thresholds)

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 014a8a5..ee22ae4 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -81,6 +84,8 @@ public class StructureChooser extends GStructureChooser implements
 
   private boolean isValidPBDEntry;
 
+  private boolean cachedPDBExists;
+
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
@@ -102,7 +107,7 @@ public class StructureChooser extends GStructureChooser implements
     }
 
     // ensure a filter option is in force for search
-    populateFilterComboBox(true);
+    populateFilterComboBox(true, cachedPDBExists);
     Thread discoverPDBStructuresThread = new Thread(new Runnable()
     {
       @Override
@@ -118,7 +123,7 @@ public class StructureChooser extends GStructureChooser implements
                 startTime);
         fetchStructuresMetaData();
         // revise filter options if no results were found
-        populateFilterComboBox(isStructuresDiscovered());
+        populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
         updateProgressIndicator(null, startTime);
         mainFrame.setVisible(true);
         updateCurrentView();
@@ -212,9 +217,9 @@ public class StructureChooser extends GStructureChooser implements
         {
           errorMsg.append(error).append("\n");
         }
-        JOptionPane.showMessageDialog(this, errorMsg.toString(),
+        JvOptionPane.showMessageDialog(this, errorMsg.toString(),
                 MessageManager.getString("label.pdb_web-service_error"),
-                JOptionPane.ERROR_MESSAGE);
+                JvOptionPane.ERROR_MESSAGE);
       }
     }
   }
@@ -237,7 +242,7 @@ public class StructureChooser extends GStructureChooser implements
         }
       }
     }
-
+    cachedPDBExists = !entries.isEmpty();
     PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
     tbl_local_pdb.setModel(tableModelx);
   }
@@ -257,7 +262,8 @@ public class StructureChooser extends GStructureChooser implements
     StringBuilder queryBuilder = new StringBuilder();
     Set<String> seqRefs = new LinkedHashSet<String>();
 
-    if (seq.getAllPDBEntries() != null)
+    if (seq.getAllPDBEntries() != null
+            && queryBuilder.length() < MAX_QLENGTH)
     {
       for (PDBEntry entry : seq.getAllPDBEntries())
       {
@@ -266,7 +272,6 @@ public class StructureChooser extends GStructureChooser implements
           queryBuilder.append("pdb_id:")
                   .append(entry.getId().toLowerCase()).append(" OR ");
           isPDBRefsFound = true;
-          // seqRefs.add(entry.getId());
         }
       }
     }
@@ -275,7 +280,8 @@ public class StructureChooser extends GStructureChooser implements
     {
       for (DBRefEntry dbRef : seq.getDBRefs())
       {
-        if (isValidSeqName(getDBRefId(dbRef)))
+        if (isValidSeqName(getDBRefId(dbRef))
+                && queryBuilder.length() < MAX_QLENGTH)
         {
           if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
           {
@@ -479,11 +485,11 @@ public class StructureChooser extends GStructureChooser implements
             {
               errorMsg.append(error).append("\n");
             }
-            JOptionPane.showMessageDialog(
+            JvOptionPane.showMessageDialog(
                     null,
                     errorMsg.toString(),
                     MessageManager.getString("label.pdb_web-service_error"),
-                    JOptionPane.ERROR_MESSAGE);
+                    JvOptionPane.ERROR_MESSAGE);
           }
         }
 
@@ -524,7 +530,8 @@ public class StructureChooser extends GStructureChooser implements
    * Populates the filter combo-box options dynamically depending on discovered
    * structures
    */
-  protected void populateFilterComboBox(boolean haveData)
+  protected void populateFilterComboBox(boolean haveData,
+          boolean cachedPDBExists)
   {
     /*
      * temporarily suspend the change listener behaviour
@@ -549,8 +556,14 @@ public class StructureChooser extends GStructureChooser implements
             VIEWS_ENTER_ID));
     cmb_filterOption.addItem(new FilterOption("From File", "-",
             VIEWS_FROM_FILE));
-    cmb_filterOption.addItem(new FilterOption("Cached PDB Entries", "-",
-            VIEWS_LOCAL_PDB));
+    FilterOption cachedOption = new FilterOption("Cached PDB Entries", "-",
+            VIEWS_LOCAL_PDB);
+    cmb_filterOption.addItem(cachedOption);
+
+    if (/*!haveData &&*/cachedPDBExists)
+    {
+      cmb_filterOption.setSelectedItem(cachedOption);
+    }
 
     cmb_filterOption.addItemListener(this);
   }
@@ -743,7 +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,
@@ -779,7 +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,
@@ -823,19 +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 });