JAL-629 Open Structure Viewer from cmdline

diff --git a/src/jalview/bin/ArgParser.java b/src/jalview/bin/ArgParser.java
index 0f9ac2e..b02bfbc 100644 (file)
--- a/src/jalview/bin/ArgParser.java
+++ b/src/jalview/bin/ArgParser.java
@@ -58,7 +58,8 @@ public class ArgParser
     ANNOTATION2, DISPLAY, GUI, NEWS, NOQUESTIONNAIRE, SORTBYTREE,
     USAGESTATS, OPEN, OPEN2, PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC,
     VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATION, NOTEMPFAC, TEMPFAC,
     ANNOTATION2, DISPLAY, GUI, NEWS, NOQUESTIONNAIRE, SORTBYTREE,
     USAGESTATS, OPEN, OPEN2, PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC,
     VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATION, NOTEMPFAC, TEMPFAC,

-    TEMPFAC_LABEL, TEMPFAC_DESC, TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP;
+    TEMPFAC_LABEL, TEMPFAC_DESC, TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP,
+    NOSTRUCTURE, STRUCTURE;

 
     static
     {
 
     static
     {

@@ -105,6 +106,8 @@ public class ArgParser
       TEMPFAC_SHADING.setOptions(Opt.STRING, Opt.LINKED);
       TITLE.setOptions(Opt.STRING, Opt.LINKED);
       PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
       TEMPFAC_SHADING.setOptions(Opt.STRING, Opt.LINKED);
       TITLE.setOptions(Opt.STRING, Opt.LINKED);
       PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);

+      NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
+      STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);

       WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
     }
 
       WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
     }
 

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 552dda6..0cdc541 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -15,8 +15,11 @@ import jalview.api.AlignmentViewPanel;
 import jalview.bin.ArgParser.Arg;
 import jalview.bin.ArgParser.ArgValues;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.bin.ArgParser.Arg;
 import jalview.bin.ArgParser.ArgValues;
 import jalview.datamodel.AlignmentAnnotation;

+import jalview.datamodel.SequenceI;

 import jalview.gui.AlignFrame;
 import jalview.gui.AlignFrame;

+import jalview.gui.AlignmentPanel;

 import jalview.gui.Desktop;
 import jalview.gui.Desktop;

+import jalview.gui.StructureChooser;

 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;

@@ -285,6 +288,87 @@ public class Commands
         }
       }
     }
         }
       }
     }

+
+    // open the structure (from same PDB file or given PDBfile)
+    if (m.get(Arg.NOSTRUCTURE) == null
+            || !m.get(Arg.NOQUESTIONNAIRE).getBoolean())
+    {
+      AlignFrame af = afMap.get(id);
+      if (m.get(Arg.STRUCTURE) != null)
+      {
+        STRUCTURE: for (String val : m.get(Arg.STRUCTURE).getValues())
+        {
+          SubId subId = new SubId(val);
+          SequenceI seq = getSpecifiedSequence(af, subId);
+          if (seq == null)
+          {
+            Console.warn("Could not find sequence for argument --"
+                    + Arg.STRUCTURE + "=" + val);
+            break STRUCTURE;
+          }
+          File structureFile = null;
+          if (subId.content != null && subId.content.length() != 0)
+          {
+            structureFile = new File(subId.content);
+            Console.debug("Using structure file (from argument) '"
+                    + structureFile.getAbsolutePath() + "'");
+          }
+          /* THIS DOESN'T WORK */
+          else if (seq.getAllPDBEntries() != null
+                  && seq.getAllPDBEntries().size() > 0)
+          {
+            structureFile = new File(
+                    seq.getAllPDBEntries().elementAt(0).getFile());
+            Console.debug("Using structure file (from sequence) '"
+                    + structureFile.getAbsolutePath() + "'");
+          }
+
+          if (structureFile == null)
+          {
+            Console.warn("Not provided structure file with '" + val + "'");
+            continue STRUCTURE;
+          }
+
+          if (!structureFile.exists())
+          {
+            Console.warn("Structure file '"
+                    + structureFile.getAbsoluteFile() + "' not found.");
+            continue STRUCTURE;
+          }
+
+          Console.debug("Using structure file "
+                  + structureFile.getAbsolutePath());
+
+          // open structure view
+          AlignmentPanel ap = af.alignPanel;
+          StructureChooser.openStructureFileForSequence(ap, seq,
+                  structureFile);
+        }
+      }
+    }
+  }
+
+  private SequenceI getSpecifiedSequence(AlignFrame af, SubId subId)
+  {
+    SequenceI seq = null;
+    SequenceI[] sequences = af.getCurrentView().getAlignment()
+            .getSequencesArray();
+    if (-1 < subId.index && subId.index < sequences.length)
+    {
+      seq = sequences[subId.index];
+    }
+    else if ("id".equals(subId.keyName))
+    {
+      for (SequenceI s : sequences)
+      {
+        if (s.getDisplayId(false).equals(subId.keyValue))
+        {
+          seq = s;
+          break;
+        }
+      }
+    }
+    return seq;

   }
 
   /**
   }
 
   /**

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 07eec2b..89d5c6b 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -24,6 +24,7 @@ package jalview.gui;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;

+import java.io.File;

 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;

@@ -116,11 +117,19 @@ public class StructureChooser extends GStructureChooser
 
   List<SequenceI> seqsWithoutSourceDBRef = null;
 
 
   List<SequenceI> seqsWithoutSourceDBRef = null;
 

+  private boolean noChooserGUI = false;
+

   private static StructureViewer lastTargetedView = null;
 
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
   private static StructureViewer lastTargetedView = null;
 
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {

+    this(selectedSeqs, selectedSeq, ap, false);
+  }
+
+  public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+          AlignmentPanel ap, boolean noChooserGUI)
+  {

     // which FTS engine to use
     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
     initDialog();
     // which FTS engine to use
     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
     initDialog();

@@ -129,6 +138,7 @@ public class StructureChooser extends GStructureChooser
     this.selectedSequence = selectedSeq;
     this.selectedSequences = selectedSeqs;
     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
     this.selectedSequence = selectedSeq;
     this.selectedSequences = selectedSeqs;
     this.progressIndicator = (ap == null) ? null : ap.alignFrame;

+    this.noChooserGUI = noChooserGUI;

     init();
 
   }
     init();
 
   }

@@ -244,7 +254,7 @@ public class StructureChooser extends GStructureChooser
     populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
     discoverStructureViews();
     updateProgressIndicator(null, startTime);
     populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
     discoverStructureViews();
     updateProgressIndicator(null, startTime);

-    mainFrame.setVisible(true);
+    mainFrame.setVisible(noChooserGUI);

     updateCurrentView();
   }
 
     updateCurrentView();
   }
 

@@ -1576,4 +1586,33 @@ public class StructureChooser extends GStructureChooser
   {
     return notQueriedTDBYet;
   }
   {
     return notQueriedTDBYet;
   }

+
+  /**
+   * Open a single structure file for a given sequence
+   */
+  public static void openStructureFileForSequence(AlignmentPanel ap,
+          SequenceI seq, File sFile)
+  {
+    StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
+            ap, true);
+    StructureSelectionManager ssm = ap.getStructureSelectionManager();
+    PDBEntry fileEntry = null;
+    try
+    {
+      fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+              sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
+              Desktop.instance);
+    } catch (Exception e)
+    {
+      Console.error("Could not open structure file '"
+              + sFile.getAbsolutePath() + "'");
+      return;
+    }
+
+    StructureViewer sViewer = sc.launchStructureViewer(ssm,
+            new PDBEntry[]
+            { fileEntry }, ap, new SequenceI[] { seq });
+
+    sc.mainFrame.dispose();
+  }

 }
 }