JAL-629 move SubId to more logical place. Attempt removal of annotations in a better...

diff --git a/src/jalview/bin/ArgParser.java b/src/jalview/bin/ArgParser.java
index b02bfbc..b18b088 100644 (file)
--- a/src/jalview/bin/ArgParser.java
+++ b/src/jalview/bin/ArgParser.java
@@ -666,4 +666,69 @@ public class ArgParser
     }
     return sb.toString();
   }
+
+  public static SubId getSubId(String item)
+  {
+    return new SubId(item);
+  }
+
+  /**
+   * 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.
+   */
+  public static class SubId
+  {
+    protected int index = 0;
+
+    protected String keyName = null;
+
+    protected String keyValue = null;
+
+    protected String content = null;
+
+    public SubId()
+    {
+    }
+
+    public SubId(String item)
+    {
+      this.parseVal(item);
+    }
+
+    public void parseVal(String item)
+    {
+      if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
+      {
+        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)
+        {
+          this.keyName = indexString.substring(0, equals);
+          this.keyValue = indexString.substring(equals + 1);
+          this.index = -1;
+        }
+        else
+        {
+          try
+          {
+            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 + "'.");
+          }
+        }
+      }
+      else
+      {
+        this.content = item;
+      }
+    }
+  }
 }
\ No newline at end of file

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 0cdc541..1f904cd 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -14,6 +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.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -148,6 +149,36 @@ 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
@@ -196,10 +227,11 @@ public class Commands
           if (m.get(Arg.TITLE) != null)
             af.setTitle(m.get(Arg.TITLE).getValue());
 
+          /* hacky approach to hiding the annotations */
           // show secondary structure annotations?
-          if (m.get(Arg.SSANNOTATION) != null
-                  && !m.get(Arg.SSANNOTATION).getBoolean())
+          if (m.get(Arg.SSANNOTATION) != null)
           {
+            boolean showSS = m.get(Arg.SSANNOTATION).getBoolean();
             // do this better (annotation types?)
             AlignmentUtils.showOrHideSequenceAnnotations(
                     af.getCurrentView().getAlignment(),
@@ -221,6 +253,9 @@ public class Commands
                     false, false);
           }
           else
+          /* comment out hacky approach up to here and add this line:
+           if (showTemperatureFactor)
+             */
           {
             if (m.get(Arg.TEMPFAC_LABEL) != null)
             {
@@ -228,9 +263,16 @@ public class Commands
                       .getFirstSequenceAnnotationOfType(
                               af.getCurrentView().getAlignment(),
                               AlignmentAnnotation.LINE_GRAPH);
+              String label = m.get(Arg.TEMPFAC_LABEL).getValue();
               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);
               }
             }
           }
@@ -274,7 +316,7 @@ public class Commands
       {
         for (String val : m.get(Arg.PAEMATRIX).getValues())
         {
-          SubId subId = new SubId(val);
+          SubId subId = ArgParser.getSubId(val);
           File paeFile = new File(subId.content);
           EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
                   paeFile, subId.index,
@@ -370,55 +412,4 @@ public class Commands
     }
     return seq;
   }
-
-  /**
-   * 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;
-
-    protected String keyName = null;
-
-    protected String keyValue = null;
-
-    protected String content = null;
-
-    protected SubId(String item)
-    {
-      if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
-      {
-        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)
-        {
-          this.keyName = indexString.substring(0, equals);
-          this.keyValue = indexString.substring(equals + 1);
-          this.index = -1;
-        }
-        else
-        {
-          try
-          {
-            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 + "'.");
-          }
-        }
-      }
-      else
-      {
-        this.content = item;
-      }
-    }
-  }
 }

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 89d5c6b..d38f39f 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1614,5 +1614,6 @@ public class StructureChooser extends GStructureChooser
             { fileEntry }, ap, new SequenceI[] { seq });
 
     sc.mainFrame.dispose();
+    sc.noChooserGUI = false;
   }
 }