JAL-629 Add image output and quit

diff --git a/src/jalview/bin/ArgParser.java b/src/jalview/bin/ArgParser.java
index b18b088..0697193 100644 (file)
--- a/src/jalview/bin/ArgParser.java
+++ b/src/jalview/bin/ArgParser.java
@@ -59,7 +59,7 @@ public class ArgParser
     USAGESTATS, OPEN, OPEN2, PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC,
     VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATION, NOTEMPFAC, TEMPFAC,
     TEMPFAC_LABEL, TEMPFAC_DESC, TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP,
-    NOSTRUCTURE, STRUCTURE;
+    NOSTRUCTURE, STRUCTURE, IMAGE, QUIT;
 
     static
     {
@@ -109,6 +109,8 @@ public class ArgParser
       NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
       STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
       WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
+      IMAGE.setOptions(Opt.STRING, Opt.LINKED);
+      QUIT.setOptions(Opt.UNARY);
     }
 
     private final String[] argNames;
@@ -667,9 +669,33 @@ public class ArgParser
     return sb.toString();
   }
 
-  public static SubId getSubId(String item)
+  // Helper methods with safety checks
+  protected static ArgValues getArgValues(Map<Arg, ArgValues> m, Arg a)
   {
-    return new SubId(item);
+    return m == null ? null : m.get(a);
+  }
+
+  public static List<String> getValues(Map<Arg, ArgValues> m, Arg a)
+  {
+    ArgValues av = getArgValues(m, a);
+    return av == null ? null : av.getValues();
+  }
+
+  public static String getValue(Map<Arg, ArgValues> m, Arg a)
+  {
+    List<String> vals = getValues(m, a);
+    return (vals == null || vals.size() == 0) ? null : vals.get(0);
+  }
+
+  public static boolean getBoolean(Map<Arg, ArgValues> m, Arg a)
+  {
+    ArgValues av = getArgValues(m, a);
+    return av == null ? false : av.getBoolean();
+  }
+
+  public static SubVal getSubVal(String item)
+  {
+    return new SubVal(item);
   }
 
   /**
@@ -678,7 +704,7 @@ public class ArgParser
    * the strings keyName and keyValue, and the content after the square brackets
    * (if present). Values not set `will be -1 or null.
    */
-  public static class SubId
+  public static class SubVal
   {
     protected int index = 0;
 
@@ -688,11 +714,7 @@ public class ArgParser
 
     protected String content = null;
 
-    public SubId()
-    {
-    }
-
-    public SubId(String item)
+    public SubVal(String item)
     {
       this.parseVal(item);
     }
@@ -719,9 +741,9 @@ public class ArgParser
             this.index = Integer.parseInt(indexString);
           } catch (NumberFormatException e)
           {
-            Console.warn("Failed to obtain sequenced id or index from '"
-                    + item + "'. Setting index=0 and using content='"
-                    + content + "'.");
+            Console.warn("Failed to obtain subvalue or index from '" + item
+                    + "'. Setting index=0 and using content='" + content
+                    + "'.");
           }
         }
       }

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 1f904cd..2a71e74 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -14,7 +14,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.ArgParser.Arg;
 import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubId;
+import jalview.bin.ArgParser.SubVal;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -26,6 +26,7 @@ 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.util.HttpUtils;
 import jalview.util.MessageManager;
@@ -59,6 +60,12 @@ public class Commands
         {
           cmds.processLinked(id);
         }
+        cmds.processImages(id);
+      }
+
+      if (argParser.getBool(Arg.QUIT))
+      {
+        Jalview.getInstance().quit();
       }
     }
   }
@@ -94,13 +101,13 @@ public class Commands
     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())
+      OPEN: for (String openFile : ArgParser.getValues(m, Arg.OPEN))
       {
         if (openFile == null)
           continue OPEN;
@@ -181,19 +188,18 @@ public class Commands
 
           // 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)
+          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 = AlignmentAnnotation.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)
@@ -218,20 +224,19 @@ public class Commands
                   tempfacType);
 
           // 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)
+          if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
           {
-            boolean showSS = m.get(Arg.SSANNOTATION).getBoolean();
             // do this better (annotation types?)
             AlignmentUtils.showOrHideSequenceAnnotations(
                     af.getCurrentView().getAlignment(),
@@ -240,8 +245,7 @@ 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<>();
@@ -257,13 +261,13 @@ public class Commands
            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 = m.get(Arg.TEMPFAC_LABEL).getValue();
+              String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
               if (aa != null)
               {
                 aa.label = label;
@@ -309,18 +313,18 @@ public class Commands
     }
 
     // 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 = ArgParser.getSubId(val);
-          File paeFile = new File(subId.content);
+          SubVal subVal = ArgParser.getSubVal(val);
+          File paeFile = new File(subVal.content);
           EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                  paeFile, subId.index,
-                  "id".equals(subId.keyName) ? subId.keyValue : null);
+                  paeFile, subVal.index,
+                  "id".equals(subVal.keyName) ? subVal.keyValue : null);
           // required to readjust the height and position of the pAE
           // annotation
           for (AlignmentViewPanel ap : af.getAlignPanels())
@@ -332,15 +336,14 @@ public class Commands
     }
 
     // open the structure (from same PDB file or given PDBfile)
-    if (m.get(Arg.NOSTRUCTURE) == null
-            || !m.get(Arg.NOQUESTIONNAIRE).getBoolean())
+    if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
     {
       AlignFrame af = afMap.get(id);
-      if (m.get(Arg.STRUCTURE) != null)
+      if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
       {
-        STRUCTURE: for (String val : m.get(Arg.STRUCTURE).getValues())
+        STRUCTURE: for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
         {
-          SubId subId = new SubId(val);
+          SubVal subId = new SubVal(val);
           SequenceI seq = getSpecifiedSequence(af, subId);
           if (seq == null)
           {
@@ -390,7 +393,57 @@ public class Commands
     }
   }
 
-  private SequenceI getSpecifiedSequence(AlignFrame af, SubId subId)
+  protected void processImages(String id)
+  {
+    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    AlignFrame af = afMap.get(id);
+
+    if (af == null)
+    {
+      Console.warn("Did not have an alignment window for id=" + id);
+      return;
+    }
+
+    if (ArgParser.getValues(m, Arg.IMAGE) != null)
+    {
+      for (String val : ArgParser.getValues(m, Arg.IMAGE))
+      {
+        SubVal subVal = new SubVal(val);
+        String type = "png"; // default
+        String fileName = subVal.content;
+        File file = new File(fileName);
+        if ("type".equals(subVal.keyName))
+        {
+          type = subVal.keyValue;
+        }
+        else if (fileName != null)
+        {
+          for (String ext : new String[] { "svg", "png", "html" })
+          {
+            if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+            {
+              type = ext;
+            }
+          }
+        }
+        switch (type)
+        {
+        case "svg":
+          af.createSVG(file);
+          break;
+        case "png":
+          af.createPNG(file);
+          break;
+        case "html":
+          HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+          htmlSVG.exportHTML(fileName);
+          break;
+        }
+      }
+    }
+  }
+
+  private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
   {
     SequenceI seq = null;
     SequenceI[] sequences = af.getCurrentView().getAlignment()