X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=2d7f02b8fad8516c14f698ad92a4be92d2b0da08;hb=453fa24ab502aaca4ffccf3590f97c897b9580b3;hp=f01b2b3b7935d51035f51db542a689386439fc08;hpb=c0e43acd458a2e19a5ab3be56a53bc88932657c4;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index f01b2b3..2d7f02b 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -14,20 +14,31 @@ 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.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
+import jalview.gui.StructureChooser;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.TFType;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.dbsources.EBIAlfaFold;
+import mc_view.PDBChain;
 
 public class Commands
 {
@@ -39,22 +50,49 @@ public class Commands
 
   private Map<String, AlignFrame> afMap;
 
-  public static void processArgs(ArgParser ap, boolean h)
+  public static boolean processArgs(ArgParser ap, boolean h)
   {
     argParser = ap;
     headless = h;
-    for (String id : argParser.linkedIds())
+    boolean argsWereParsed = false;
+    if (headless)
     {
-      Commands cmds = new Commands();
-      if (id == null)
-      {
-        cmds.processUnlinked(id);
-      }
-      else
+      System.setProperty("java.awt.headless", "true");
+    }
+
+    if (argParser != null && argParser.linkedIds() != null)
+    {
+      for (String id : argParser.linkedIds())
       {
-        cmds.processLinked(id);
+        Console.debug("##### id=" + id);
+        Commands cmds = new Commands();
+        if (id == null)
+        {
+          cmds.processUnlinked(id);
+        }
+        else
+        {
+          cmds.processLinked(id);
+        }
+        cmds.processImages(id);
+        argsWereParsed |= cmds.wereParsed();
       }
+
     }
+    if (argParser.getBool(Arg.QUIT))
+    {
+      Jalview.getInstance().quit();
+      return true;
+    }
+    // carry on with jalview.bin.Jalview
+    return argsWereParsed;
+  }
+
+  boolean argsWereParsed = false;
+
+  private boolean wereParsed()
+  {
+    return argsWereParsed;
   }
 
   public Commands()
@@ -70,6 +108,8 @@ public class Commands
 
   protected void processUnlinked(String id)
   {
+    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+
     processLinked(id);
   }
 
@@ -87,18 +127,18 @@ public class Commands
     FileFormatI format = null;
     DataSourceType protocol = null;
     */
-
-    if (m.get(Arg.OPEN) != null)
+    if (ArgParser.getArgValues(m, Arg.OPEN) != null)
     {
       long progress = -1;
 
       boolean first = true;
       AlignFrame af;
-      OPEN: for (String openFile : m.get(Arg.OPEN).getValues())
+      for (String openFile : ArgParser.getValues(m, Arg.OPEN))
       {
         if (openFile == null)
-          continue OPEN;
+          continue;
 
+        argsWereParsed = true;
         if (first)
         {
           first = false;
@@ -123,7 +163,6 @@ public class Commands
             if (!(new File(openFile)).exists())
             {
               Console.warn("Can't find file '" + openFile + "'");
-              continue OPEN;
             }
           }
         }
@@ -143,27 +182,56 @@ public class Commands
         af = afMap.get(id);
         if (af == null)
         {
+          /*
+           * this approach isn't working yet
+          // get default annotations before opening AlignFrame
+          if (m.get(Arg.SSANNOTATION) != null)
+          {
+            Console.debug("***** SSANNOTATION="
+                    + m.get(Arg.SSANNOTATION).getBoolean());
+          }
+          if (m.get(Arg.NOTEMPFAC) != null)
+          {
+            Console.debug(
+                    "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
+          }
+          boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
+                  ? m.get(Arg.SSANNOTATION).getBoolean()
+                  : false;
+          boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
+                  ? !m.get(Arg.NOTEMPFAC).getBoolean()
+                  : false;
+          Console.debug("***** tempfac=" + showTemperatureFactor
+                  + ", showSS=" + showSecondaryStructure);
+          StructureSelectionManager ssm = StructureSelectionManager
+                  .getStructureSelectionManager(Desktop.instance);
+          if (ssm != null)
+          {
+            ssm.setAddTempFacAnnot(showTemperatureFactor);
+            ssm.setProcessSecondaryStructure(showSecondaryStructure);
+          }
+           */
+
           // get kind of temperature factor annotation
-          AlignmentAnnotation.TFType tempfacType = null;
-          if ((m.get(Arg.NOTEMPFAC) == null
-                  || !m.get(Arg.NOTEMPFAC).getBoolean())
-                  && m.get(Arg.TEMPFAC) != null)
+          StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
+          if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+                  && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
           {
             try
             {
-              tempfacType = AlignmentAnnotation.TFType
-                      .valueOf(m.get(Arg.TEMPFAC).getValue()
-                              .toUpperCase(Locale.ROOT));
+              tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
+                      .getValue(m, Arg.TEMPFAC).toUpperCase(Locale.ROOT));
               Console.debug("Obtained Temperature Factor type of '"
                       + tempfacType + "'");
             } catch (IllegalArgumentException e)
             {
+              // Just an error message!
               StringBuilder sb = new StringBuilder().append("Cannot set --")
                       .append(Arg.TEMPFAC.getName()).append(" to '")
                       .append(tempfacType)
                       .append("', ignoring.  Valid values are: ");
-              Iterator<AlignmentAnnotation.TFType> it = Arrays
-                      .stream(AlignmentAnnotation.TFType.values())
+              Iterator<StructureImportSettings.TFType> it = Arrays
+                      .stream(StructureImportSettings.TFType.values())
                       .iterator();
               while (it.hasNext())
               {
@@ -178,22 +246,25 @@ public class Commands
           Console.debug(
                   "Opening '" + openFile + "' in new alignment frame");
           FileLoader fileLoader = new FileLoader(!headless);
-          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
-                  tempfacType);
+
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+
+          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+                  format);
 
           // wrap alignment?
-          if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean())
+          if (ArgParser.getBoolean(m, Arg.WRAP))
           {
             af.getCurrentView().setWrapAlignment(true);
           }
 
           // change alignment frame title
-          if (m.get(Arg.TITLE) != null)
-            af.setTitle(m.get(Arg.TITLE).getValue());
+          if (ArgParser.getValue(m, Arg.TITLE) != null)
+            af.setTitle(ArgParser.getValue(m, Arg.TITLE));
 
+          /* hacky approach to hiding the annotations */
           // show secondary structure annotations?
-          if (m.get(Arg.SSANNOTATION) != null
-                  && !m.get(Arg.SSANNOTATION).getBoolean())
+          if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
           {
             // do this better (annotation types?)
             AlignmentUtils.showOrHideSequenceAnnotations(
@@ -203,35 +274,53 @@ public class Commands
           }
 
           // show temperature factor annotations?
-          if (m.get(Arg.NOTEMPFAC) != null
-                  && m.get(Arg.NOTEMPFAC).getBoolean())
+          if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
           {
             // do this better (annotation types?)
             List<String> hideThese = new ArrayList<>();
             hideThese.add("Temperature Factor");
-            hideThese.add(MessageManager
-                    .getString("label.alphafold_reliability"));
+            hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
             AlignmentUtils.showOrHideSequenceAnnotations(
                     af.getCurrentView().getAlignment(), hideThese, null,
                     false, false);
           }
           else
+          /* comment out hacky approach up to here and add this line:
+           if (showTemperatureFactor)
+             */
           {
-            if (m.get(Arg.TEMPFAC_LABEL) != null)
+            if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
             {
               AlignmentAnnotation aa = AlignmentUtils
                       .getFirstSequenceAnnotationOfType(
                               af.getCurrentView().getAlignment(),
                               AlignmentAnnotation.LINE_GRAPH);
+              String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
               if (aa != null)
               {
-                aa.label = m.get(Arg.TEMPFAC_LABEL).getValue();
+                aa.label = label;
+              }
+              else
+              {
+                Console.info(
+                        "Could not find annotation to apply tempfac_label '"
+                                + label);
               }
             }
           }
 
           // store the AlignFrame for this id
           afMap.put(id, af);
+
+          // is it its own structure file?
+          if (format.isStructureFile())
+          {
+            StructureSelectionManager ssm = StructureSelectionManager
+                    .getStructureSelectionManager(Desktop.instance);
+            SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
+            ssm.computeMapping(false, new SequenceI[] { seq }, null,
+                    openFile, DataSourceType.FILE, null);
+          }
         }
         else
         {
@@ -251,31 +340,55 @@ public class Commands
           Console.error("Could not open any files in headless mode");
           System.exit(1);
         }
-      }
-      else
-      {
-        Console.warn("No more files to open");
-        if (desktop != null)
-          desktop.setProgressBar(null, progress);
+        else
+        {
+          Console.warn("No more files to open");
+          if (desktop != null)
+            desktop.setProgressBar(null, progress);
+        }
       }
 
     }
 
     // load a pAE file if given
-    if (m.get(Arg.PAEMATRIX) != null)
+    if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
     {
       AlignFrame af = afMap.get(id);
       if (af != null)
       {
-        for (String val : m.get(Arg.PAEMATRIX).getValues())
+        for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
         {
-          SubId subId = new SubId(val);
-          File paeFile = new File(subId.content);
-          EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                  paeFile, subId.index,
-                  "id".equals(subId.keyName) ? subId.keyValue : null);
-          // required to readjust the height and position of the pAE
-          // annotation
+          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();
@@ -283,74 +396,153 @@ public class Commands
         }
       }
     }
-  }
 
-  /**
-   * A helper class to parse a string of the possible forms "content"
-   * "[index]content", "[keyName=keyValue]content" and return the integer index,
-   * the strings keyName and keyValue, and the content after the square brackets
-   * (if present). Values not set will be -1 or null.
-   */
-  protected class SubId
-  {
-    protected int index = 0;
+    // open the structure (from same PDB file or given PDBfile)
+    if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
+    {
+      AlignFrame af = afMap.get(id);
+      if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
+      {
+        for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
+        {
+          SubVal subId = new SubVal(val);
+          SequenceI seq = getSpecifiedSequence(af, subId);
+          if (seq == null)
+          {
+            Console.warn("Could not find sequence for argument --"
+                    + Arg.STRUCTURE + "=" + val);
+            // you probably want to continue here, not break
+            // break;
+            continue;
+          }
+          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;
+          }
+
+          if (!structureFile.exists())
+          {
+            Console.warn("Structure file '"
+                    + structureFile.getAbsoluteFile() + "' not found.");
+            continue;
+          }
+
+          Console.debug("Using structure file "
+                  + structureFile.getAbsolutePath());
+
+          // open structure view
+          AlignmentPanel ap = af.alignPanel;
+          StructureChooser.openStructureFileForSequence(ap, seq,
+                  structureFile);
+        }
+      }
+    }
 
-    protected String keyName = null;
+    boolean doShading = ArgParser.getBoolean(m, Arg.TEMPFAC_SHADING);
+    if (doShading)
+    {
+      AlignFrame af = afMap.get(id);
+      for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+              .findAnnotation(PDBChain.class.getName().toString()))
+      {
+        AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+                af.alignPanel.av.getGlobalColourScheme(), 0);
+        acg.setSeqAssociated(true);
+        af.changeColour(acg);
+        Console.info("Changed colour " + acg.toString());
+      }
+    }
+  }
 
-    protected String keyValue = null;
+  protected void processImages(String id)
+  {
+    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    AlignFrame af = afMap.get(id);
 
-    protected String content = null;
+    if (af == null)
+    {
+      Console.warn("Did not have an alignment window for id=" + id);
+      return;
+    }
 
-    protected SubId(String item)
+    if (ArgParser.getValues(m, Arg.IMAGE) != null)
     {
-      if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
+      for (String val : ArgParser.getValues(m, Arg.IMAGE))
       {
-        int openBracket = item.indexOf('[');
-        int closeBracket = item.indexOf(']');
-        String indexString = item.substring(openBracket + 1, closeBracket);
-        this.content = item.substring(closeBracket + 1);
-        int equals = indexString.indexOf('=');
-        if (equals > -1)
+        SubVal subVal = new SubVal(val);
+        String type = "png"; // default
+        String fileName = subVal.content;
+        File file = new File(fileName);
+        if ("type".equals(subVal.keyName))
         {
-          this.keyName = indexString.substring(0, equals);
-          this.keyValue = indexString.substring(equals + 1);
-          this.index = -1;
+          type = subVal.keyValue;
         }
-        else
+        else if (fileName != null)
         {
-          try
-          {
-            this.index = Integer.parseInt(indexString);
-          } catch (NumberFormatException e)
+          for (String ext : new String[] { "svg", "png", "html" })
           {
-            Console.warn("Failed to obtain sequenced id or index from '"
-                    + item + "'. Setting index=0 and using content='"
-                    + content + "'.");
+            if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+            {
+              type = ext;
+            }
           }
         }
-      }
-      else
-      {
-        this.content = item;
+        // for moment we disable JSON export
+        Cache.setPropsAreReadOnly(true);
+        Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
+        switch (type)
+        {
+        case "svg":
+          Console.debug("Outputting type '" + type + "' to " + fileName);
+          af.createSVG(file);
+          break;
+        case "png":
+          Console.debug("Outputting type '" + type + "' to " + fileName);
+          af.createPNG(file);
+          break;
+        case "html":
+          Console.debug("Outputting type '" + type + "' to " + fileName);
+          HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+          htmlSVG.exportHTML(fileName);
+          break;
+        default:
+          Console.warn("--image type '" + type + "' not known. Ignoring");
+          break;
+        }
       }
     }
   }
 
-  private void testMethod()
+  private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
   {
-    Desktop Jalview = Desktop.instance;
-    jalview.bin.Cache.setProperty("SVG_RENDERING", "Text");
-    for (AlignFrame af : Jalview.getAlignFrames())
+    AlignmentI al = af.getCurrentView().getAlignment();
+    if (-1 < subId.index && subId.index < al.getSequences().size())
+    {
+      return al.getSequenceAt(subId.index);
+    }
+    else if ("id".equals(subId.keyName))
     {
-      String title = af.getTitle();
-      System.out.println("Title: " + af.getTitle());
-      AlignViewport view = af.getCurrentView();
-      view.setShowText(false);
-      view.setShowAnnotation(false);
-      af.deselectAllSequenceMenuItem_actionPerformed(null);
-      af.repaint();
-      af.createPNG(new File(title + ".png"));
-      af.createSVG(new File(title + ".svg"));
+      return al.findName(subId.keyValue);
     }
+    return null;
   }
 }