X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=26ce8c32c1709ebfa7d81a923b8d4271947392a0;hb=a5928e2c1b9e2cea8d9c43f3d03f9cce2604f3b2;hp=2d7f02b8fad8516c14f698ad92a4be92d2b0da08;hpb=08646d1f0486e645adeaf4ea9a6c0f6b599f980c;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 2d7f02b..26ce8c3 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -1,6 +1,7 @@
 package jalview.bin;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -13,16 +14,21 @@ import java.util.Map;
 import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubVal;
+import jalview.bin.ArgParser.ArgValue;
+import jalview.bin.ArgParser.ArgValuesMap;
+import jalview.bin.ArgParser.SubVals;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
+import jalview.gui.AssociatePdbFileWithSeq;
 import jalview.gui.Desktop;
+import jalview.gui.Preferences;
 import jalview.gui.StructureChooser;
+import jalview.gui.StructureViewer;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -44,38 +50,65 @@ public class Commands
 {
   Desktop desktop;
 
-  private static boolean headless;
+  private boolean headless;
 
-  private static ArgParser argParser;
+  private ArgParser argParser;
 
   private Map<String, AlignFrame> afMap;
 
-  public static boolean processArgs(ArgParser ap, boolean h)
+  private boolean commandArgsProvided = false;
+
+  private boolean argsWereParsed = false;
+
+  public Commands(ArgParser argparser, boolean headless)
+  {
+    this(Desktop.instance, argparser, headless);
+  }
+
+  public Commands(Desktop d, ArgParser argparser, boolean h)
   {
-    argParser = ap;
+    argParser = argparser;
     headless = h;
-    boolean argsWereParsed = false;
-    if (headless)
+    desktop = d;
+    afMap = new HashMap<String, AlignFrame>();
+    if (argparser != null)
     {
-      System.setProperty("java.awt.headless", "true");
+      processArgs(argparser, headless);
     }
+  }
+
+  private boolean processArgs(ArgParser argparser, boolean h)
+  {
+    argParser = argparser;
+    headless = h;
+    boolean theseArgsWereParsed = false;
 
     if (argParser != null && argParser.linkedIds() != null)
     {
       for (String id : argParser.linkedIds())
       {
-        Console.debug("##### id=" + id);
-        Commands cmds = new Commands();
+        ArgValuesMap avm = argParser.linkedArgs(id);
+        theseArgsWereParsed = true;
         if (id == null)
         {
-          cmds.processUnlinked(id);
+          theseArgsWereParsed &= processUnlinked(id);
         }
         else
         {
-          cmds.processLinked(id);
+          theseArgsWereParsed &= processLinked(id);
+        }
+        theseArgsWereParsed &= processImages(id);
+
+        // close ap
+        if (avm.getBoolean(Arg.CLOSE))
+        {
+          AlignFrame af = afMap.get(id);
+          if (af != null)
+          {
+            af.closeMenuItem_actionPerformed(true);
+          }
         }
-        cmds.processImages(id);
-        argsWereParsed |= cmds.wereParsed();
+
       }
 
     }
@@ -85,37 +118,31 @@ public class Commands
       return true;
     }
     // carry on with jalview.bin.Jalview
+    argsWereParsed = theseArgsWereParsed;
     return argsWereParsed;
   }
 
-  boolean argsWereParsed = false;
-
-  private boolean wereParsed()
-  {
-    return argsWereParsed;
-  }
-
-  public Commands()
+  public boolean commandArgsProvided()
   {
-    this(Desktop.instance);
+    return commandArgsProvided;
   }
 
-  public Commands(Desktop d)
+  public boolean argsWereParsed()
   {
-    this.desktop = d;
-    afMap = new HashMap<String, AlignFrame>();
+    return argsWereParsed;
   }
 
-  protected void processUnlinked(String id)
+  protected boolean processUnlinked(String id)
   {
-    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
-
-    processLinked(id);
+    return processLinked(id);
   }
 
-  protected void processLinked(String id)
+  protected boolean processLinked(String id)
   {
-    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    boolean theseArgsWereParsed = false;
+    ArgValuesMap avm = argParser.linkedArgs(id);
+    if (avm == null)
+      return true;
 
     /*
     // script to execute after all loading is completed one way or another
@@ -127,27 +154,31 @@ public class Commands
     FileFormatI format = null;
     DataSourceType protocol = null;
     */
-    if (ArgParser.getArgValues(m, Arg.OPEN) != null)
+    if (avm.containsArg(Arg.OPEN))
     {
+      commandArgsProvided = true;
       long progress = -1;
 
       boolean first = true;
+      boolean progressBarSet = false;
       AlignFrame af;
-      for (String openFile : ArgParser.getValues(m, Arg.OPEN))
+      for (ArgValue av : avm.getArgValueList(Arg.OPEN))
       {
+        String openFile = av.getValue();
         if (openFile == null)
           continue;
 
-        argsWereParsed = true;
+        theseArgsWereParsed = true;
         if (first)
         {
           first = false;
-          if (!headless)
+          if (!headless && desktop != null)
           {
             desktop.setProgressBar(
                     MessageManager.getString(
                             "status.processing_commandline_args"),
                     progress = System.currentTimeMillis());
+            progressBarSet = true;
           }
         }
 
@@ -214,13 +245,14 @@ public class Commands
 
           // get kind of temperature factor annotation
           StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
-          if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
-                  && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
+          if ((!avm.getBoolean(Arg.NOTEMPFAC))
+                  && avm.containsArg(Arg.TEMPFAC))
           {
             try
             {
-              tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
-                      .getValue(m, Arg.TEMPFAC).toUpperCase(Locale.ROOT));
+              tempfacType = StructureImportSettings.TFType
+                      .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
+                              .toUpperCase(Locale.ROOT));
               Console.debug("Obtained Temperature Factor type of '"
                       + tempfacType + "'");
             } catch (IllegalArgumentException e)
@@ -253,18 +285,24 @@ public class Commands
                   format);
 
           // wrap alignment?
-          if (ArgParser.getBoolean(m, Arg.WRAP))
+          if (avm.getBoolean(Arg.WRAP))
           {
             af.getCurrentView().setWrapAlignment(true);
           }
 
+          // colour aligment?
+          if (avm.containsArg(Arg.COLOUR))
+          {
+            af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
+          }
+
           // change alignment frame title
-          if (ArgParser.getValue(m, Arg.TITLE) != null)
-            af.setTitle(ArgParser.getValue(m, Arg.TITLE));
+          if (avm.containsArg(Arg.TITLE))
+            af.setTitle(avm.getValue(Arg.TITLE));
 
           /* hacky approach to hiding the annotations */
           // show secondary structure annotations?
-          if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
+          if (avm.getBoolean(Arg.SSANNOTATION))
           {
             // do this better (annotation types?)
             AlignmentUtils.showOrHideSequenceAnnotations(
@@ -274,7 +312,7 @@ public class Commands
           }
 
           // show temperature factor annotations?
-          if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+          if (avm.getBoolean(Arg.NOTEMPFAC))
           {
             // do this better (annotation types?)
             List<String> hideThese = new ArrayList<>();
@@ -289,13 +327,13 @@ public class Commands
            if (showTemperatureFactor)
              */
           {
-            if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
+            if (avm.containsArg(Arg.TEMPFAC_LABEL))
             {
               AlignmentAnnotation aa = AlignmentUtils
                       .getFirstSequenceAnnotationOfType(
                               af.getCurrentView().getAlignment(),
                               AlignmentAnnotation.LINE_GRAPH);
-              String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
+              String label = avm.getValue(Arg.TEMPFAC_LABEL);
               if (aa != null)
               {
                 aa.label = label;
@@ -319,18 +357,17 @@ public class Commands
                     .getStructureSelectionManager(Desktop.instance);
             SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
             ssm.computeMapping(false, new SequenceI[] { seq }, null,
-                    openFile, DataSourceType.FILE, null);
+                    openFile, DataSourceType.FILE, null, null, null);
           }
         }
         else
         {
           Console.debug(
                   "Opening '" + openFile + "' in existing alignment frame");
-          af.getCurrentView().addFile(new File(openFile), format);
+          af.getCurrentView().addFile(new File(openFile), format, false);
         }
 
-        System.out
-                .println("Command " + Arg.OPEN + " executed successfully!");
+        Console.debug("Command " + Arg.OPEN + " executed successfully!");
 
       }
       if (first) // first=true means nothing opened
@@ -343,69 +380,24 @@ public class Commands
         else
         {
           Console.warn("No more files to open");
-          if (desktop != null)
-            desktop.setProgressBar(null, progress);
         }
       }
+      if (progressBarSet && desktop != null)
+        desktop.setProgressBar(null, progress);
 
     }
 
-    // load a pAE file if given
-    if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
-    {
-      AlignFrame af = afMap.get(id);
-      if (af != null)
-      {
-        for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
-        {
-          SubVal subVal = ArgParser.getSubVal(val);
-          File paeFile = new File(subVal.content);
-          String structId = "structid".equals(subVal.keyName)
-                  ? subVal.keyValue
-                  : null;
-          if (subVal.notSet())
-          {
-            // take structid from pdbfilename
-          }
-          if ("structfile".equals(subVal.keyName))
-          {
-            EBIAlfaFold.addAlphaFoldPAEToStructure(
-                    af.getCurrentView().getAlignment(), paeFile,
-                    subVal.index, subVal.keyValue, false);
-          }
-          else if ("structid".equals(subVal.keyName))
-          {
-            EBIAlfaFold.addAlphaFoldPAEToStructure(
-                    af.getCurrentView().getAlignment(), paeFile,
-                    subVal.index, subVal.keyValue, true);
-          }
-          else
-          {
-            EBIAlfaFold.addAlphaFoldPAEToSequence(
-                    af.getCurrentView().getAlignment(), paeFile,
-                    subVal.index,
-                    "seqid".equals(subVal.keyName) ? subVal.keyValue
-                            : null);
-            // required to readjust the height and position of the pAE
-            // annotation
-          }
-          for (AlignmentViewPanel ap : af.getAlignPanels())
-          {
-            ap.adjustAnnotationHeight();
-          }
-        }
-      }
-    }
-
     // open the structure (from same PDB file or given PDBfile)
-    if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
+    if (!avm.getBoolean(Arg.NOSTRUCTURE))
     {
       AlignFrame af = afMap.get(id);
-      if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
+      if (avm.containsArg(Arg.STRUCTURE))
       {
-        for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
+        commandArgsProvided = true;
+        for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
         {
-          SubVal subId = new SubVal(val);
+          String val = av.getValue();
+          SubVals subId = new SubVals(val);
           SequenceI seq = getSpecifiedSequence(af, subId);
           if (seq == null)
           {
@@ -416,12 +408,27 @@ public class Commands
             continue;
           }
           File structureFile = null;
-          if (subId.content != null && subId.content.length() != 0)
+          if (subId.getContent() != null
+                  && subId.getContent().length() != 0)
           {
-            structureFile = new File(subId.content);
+            structureFile = new File(subId.getContent());
             Console.debug("Using structure file (from argument) '"
                     + structureFile.getAbsolutePath() + "'");
           }
+
+          // TRY THIS
+          /*
+           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+                  .associatePdbWithSeq(selectedPdbFileName,
+                          DataSourceType.FILE, selectedSequence, true,
+                          Desktop.instance);
+                          
+           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
+                  ap, new SequenceI[]
+                  { selectedSequence });
+          
+           */
+
           /* THIS DOESN'T WORK */
           else if (seq.getAllPDBEntries() != null
                   && seq.getAllPDBEntries().size() > 0)
@@ -448,15 +455,90 @@ public class Commands
           Console.debug("Using structure file "
                   + structureFile.getAbsolutePath());
 
+          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+                  .associatePdbWithSeq(structureFile.getAbsolutePath(),
+                          DataSourceType.FILE, seq, true, Desktop.instance);
+
           // open structure view
           AlignmentPanel ap = af.alignPanel;
-          StructureChooser.openStructureFileForSequence(ap, seq,
-                  structureFile);
+          if (headless)
+          {
+            Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+                    StructureViewer.ViewerType.JMOL.toString());
+          }
+
+          // get tft, paeFilename, label?
+          /*
+          ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
+                  Arg.TEMPFAC);
+           */
+          StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+                  false, structureFile.getAbsolutePath(), null, null); // tft,
+                                                                       // paeFilename);
         }
       }
     }
 
-    boolean doShading = ArgParser.getBoolean(m, Arg.TEMPFAC_SHADING);
+    // load a pAE file if given
+    if (avm.containsArg(Arg.PAEMATRIX))
+    {
+      AlignFrame af = afMap.get(id);
+      if (af != null)
+      {
+        for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
+        {
+          String val = av.getValue();
+          SubVals subVals = ArgParser.getSubVals(val);
+          File paeFile = new File(subVals.getContent());
+          String paePath = null;
+          try
+          {
+            paePath = paeFile.getCanonicalPath();
+          } catch (IOException e)
+          {
+            paePath = paeFile.getAbsolutePath();
+            Console.warn(
+                    "Problem with the PAE file path: '" + paePath + "'");
+          }
+          String structId = subVals.get("structid");
+          if (subVals.notSet())
+          {
+            // take structid from pdbfilename
+          }
+          if (subVals.has("structfile"))
+          {
+            Console.info("***** Attaching paeFile '" + paePath + "' to "
+                    + "structfile=" + subVals.get("structfile"));
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), subVals.get("structfile"),
+                    true, false);
+          }
+          else if (subVals.has("structid"))
+          {
+            Console.info("***** Attaching paeFile '" + paePath + "' to "
+                    + "structid=" + subVals.get("structid"));
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), subVals.get("structid"),
+                    true, true);
+          }
+          else
+          {
+            Console.debug("***** Attaching paeFile '" + paePath
+                    + "' to sequence index " + subVals.getIndex());
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile, subVals.getIndex(), null, false, false);
+            // required to readjust the height and position of the pAE
+            // annotation
+          }
+          for (AlignmentViewPanel ap : af.getAlignPanels())
+          {
+            ap.adjustAnnotationHeight();
+          }
+        }
+      }
+    }
+
+    boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
     if (doShading)
     {
       AlignFrame af = afMap.get(id);
@@ -470,30 +552,33 @@ public class Commands
         Console.info("Changed colour " + acg.toString());
       }
     }
+
+    return theseArgsWereParsed;
   }
 
-  protected void processImages(String id)
+  protected boolean processImages(String id)
   {
-    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.linkedArgs(id);
     AlignFrame af = afMap.get(id);
 
     if (af == null)
     {
       Console.warn("Did not have an alignment window for id=" + id);
-      return;
+      return false;
     }
 
-    if (ArgParser.getValues(m, Arg.IMAGE) != null)
+    if (avm.containsArg(Arg.IMAGE))
     {
-      for (String val : ArgParser.getValues(m, Arg.IMAGE))
+      for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
       {
-        SubVal subVal = new SubVal(val);
+        String val = av.getValue();
+        SubVals subVal = new SubVals(val);
         String type = "png"; // default
-        String fileName = subVal.content;
+        String fileName = subVal.getContent();
         File file = new File(fileName);
-        if ("type".equals(subVal.keyName))
+        if (subVal.has("type"))
         {
-          type = subVal.keyValue;
+          type = subVal.get("type");
         }
         else if (fileName != null)
         {
@@ -530,18 +615,20 @@ public class Commands
         }
       }
     }
+    return true;
   }
 
-  private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
+  private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
   {
     AlignmentI al = af.getCurrentView().getAlignment();
-    if (-1 < subId.index && subId.index < al.getSequences().size())
+    if (-1 < subId.getIndex()
+            && subId.getIndex() < al.getSequences().size())
     {
-      return al.getSequenceAt(subId.index);
+      return al.getSequenceAt(subId.getIndex());
     }
-    else if ("id".equals(subId.keyName))
+    else if (subId.has("seqid"))
     {
-      return al.findName(subId.keyValue);
+      return al.findName(subId.get("seqid"));
     }
     return null;
   }