JAL-904 added scrollToRow and scrollToColumn methods to javascript API and reintroduc...

diff --git a/examples/jalviewLiteJs.html b/examples/jalviewLiteJs.html
index 434d1a7..2a90393 100644 (file)
--- a/examples/jalviewLiteJs.html
+++ b/examples/jalviewLiteJs.html
@@ -304,6 +304,14 @@ public boolean addPdbFile(AlignFrame alFrame,
 // the given location the top left hand corner for given current view (v2.7)
 public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn)
 
+// adjust horizontal scroll in alf to the make 
+// the given location the left hand corner for given current view (v2.7)
+public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
+
+// adjust horizontal/vertical scroll in alf to the make 
+// the given location the top row for given current view (v2.7)
+public void scrollViewToRowIn(AlignFrame alf, String topRow)
+
 
 // return separator separated list of feature groups 
 // on the current alignment

diff --git a/examples/javascript/jalview.js b/examples/javascript/jalview.js
index 4cc613e..66c5a3e 100644 (file)
--- a/examples/javascript/jalview.js
+++ b/examples/javascript/jalview.js
@@ -17,11 +17,11 @@ function getDestinationFrms(source, frames) {
        var frid = "";\r
        for (frm in frames) {\r
                try {\r
-                       frid = (("" + source.getDatasetId()) == ("" + frames[frm]\r
-                                       .getDatasetId()));\r
+                       frid = (source!=null) && (("" + source.getSequenceSetId()) == ("" + frames[frm].currentAlignFrame\r
+                                       .getSequenceSetId()));\r
                } catch (q) {\r
-               }\r
-               ;\r
+               };\r
+               \r
                if (!frames[frm].equals(source) && !frid\r
                                && !frames[frm].currentAlignFrame.equals(source)) {\r
                        frms[frms.length] = frames[frm];\r
@@ -108,6 +108,7 @@ function linkJvJmol(applet, jmolView, modeltofiles) {
        // try { applet.setViewListener("viewlist"); } catch (err) {};\r
        if (jmolView)\r
        {\r
+               var sep = applet.getSeparator();\r
                var oldjm=jmolView;\r
                // recover full id of Jmol applet\r
                jmolView=_jmolGetApplet(jmolView).id;\r
@@ -129,14 +130,15 @@ function linkJvJmol(applet, jmolView, modeltofiles) {
                mtf="";\r
                var dbase = document.baseURI.substring(0,document.baseURI.lastIndexOf("/")+1);\r
                for (m in jmbinding._modelstofiles)\r
-               { mtf+=jmbinding._modelstofiles[m];\r
+               { if (m>0) { mtf+=sep; }\r
+               mtf+=jmbinding._modelstofiles[m];\r
                if (jmbinding._modelstofiles[m].indexOf("//")==-1)\r
-                       { jmbinding._fullmpath[m] = dbase+jmbinding._modelstofiles[m]; }\r
-                 jmbinding._filetonum.put(jmbinding._modelstofiles[m], m);\r
-                 jmbinding._filetonum.put(jmbinding._fullmpath[m], m);\r
+                       { jmbinding._fullmpath[m] = dbase+((jmbinding._modelstofiles[m].indexOf("/")==0) ? jmbinding._modelstofiles[m].substring(1) : jmbinding._modelstofiles[m]); }\r
+                 jmbinding._filetonum.put(jmbinding._modelstofiles[m], m+1); \r
+                 jmbinding._filetonum.put(jmbinding._fullmpath[m], m+1);\r
                  \r
-                 if (m>0) { mtf+=sep; }}\r
-               jvfollower.setStructureListener("_structure", mtf);\r
+                 }\r
+               applet.setStructureListener("_structure", mtf);\r
        }\r
 }\r
 \r
@@ -265,10 +267,11 @@ function _jmolhover(jmid, atomlabel, atomidx) {
        // relaxed third parameter - may be null or a model number for multi model\r
        // views\r
        atomlabel = ("" + atomlabel)\r
-                       .match(/\[(.+)\](\d+):(.)\.(\S+)\s*(\/\d+\.|).+/);\r
+                       .match(/\[(.+)\](\d+):(.)\.([^\/]+)(\/\d+\.|).+/);\r
        atomidx = "" + atomidx;\r
        if (atomlabel[5]) {\r
                atomlabel[5] = atomlabel[5].match(/\/(.+)\./)[1];\r
+               atomlabel[5] = parseInt(atomlabel[5])-1;\r
        } else {\r
                // default - first model\r
                atomlabel[5] = 0;\r
@@ -278,7 +281,8 @@ function _jmolhover(jmid, atomlabel, atomidx) {
                _jvapps[ap].mouseOverStructure(atomlabel[2], atomlabel[3],\r
                                document.baseURI\r
                                                .substring(0, document.baseURI.lastIndexOf('/'))\r
-                                               + "/" + modeltofiles[atomlabel[5]]);\r
+                                               + "/" + \r
+                                               modeltofiles[atomlabel[5]]);\r
                msg = _jmolhovermsg;\r
        }\r
 }\r

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 8f8ac5a..d2b04f9 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -3543,4 +3543,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {\r
     alignPanel.seqPanel.scrollTo(row, column);    \r
   }\r
+  public void scrollToRow(int row)\r
+  {\r
+    alignPanel.seqPanel.scrollToRow(row);    \r
+  }\r
+  public void scrollToColumn(int column)\r
+  {\r
+    alignPanel.seqPanel.scrollToColumn(column);    \r
+  }\r
+  /**\r
+   * @return the alignments unique ID.\r
+   */\r
+  public String getSequenceSetId() {\r
+    return viewport.getSequenceSetId();\r
+  }\r
 }\r

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index ade0afd..cce8c23 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1774,8 +1774,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     if (repaint)
     {
+      ap.scalePanelHolder.repaint();
       ap.repaint();
-      //ap.paintAlignment(false);
     }
   }
 
@@ -1791,5 +1791,25 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     column = column<0 ? ap.av.startRes : column;
     ap.scrollTo(row, row, column, true, true);
   }
+  /**
+   * scroll to the given row - or nearest visible location
+   * @param row
+   */
+  public void scrollToRow(int row)
+  {
+    
+    row = row<0 ? ap.av.startSeq : row;
+    ap.scrollTo(row, row, ap.av.startRes, true, true);
+  }
+  /**
+   * scroll to the given column - or nearest visible location
+   * @param column
+   */
+  public void scrollToColumn(int column)
+  {
+    
+    column = column<0 ? ap.av.startRes : column;
+    ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true);
+  }
 
 }

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 24f3351..25c907d 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -69,6 +69,10 @@ import netscape.javascript.JSObject;
 public class JalviewLite extends Applet implements StructureSelectionManagerProvider, JalviewLiteJsApi\r
 {\r
 \r
+  public StructureSelectionManager getStructureSelectionManager()\r
+  {\r
+    return StructureSelectionManager.getStructureSelectionManager(this);\r
+  }\r
   // /////////////////////////////////////////\r
   // The following public methods maybe called\r
   // externally, eg via javascript in HTML page\r
@@ -934,11 +938,44 @@ public class JalviewLite extends Applet implements StructureSelectionManagerProv
       \r
     } catch (Exception ex)\r
     {\r
-      System.err.println("Couldn't parse integer arguments (topRow='"+topRow+"' and leftHandColumn='"+leftHandColumn+"'");\r
+      System.err.println("Couldn't parse integer arguments (topRow='"+topRow+"' and leftHandColumn='"+leftHandColumn+"')");\r
+      ex.printStackTrace();\r
+    }\r
+  }\r
+\r
+  /* (non-Javadoc)\r
+   * @see jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui.AlignFrame, java.lang.String)\r
+   */\r
+  @Override\r
+  public void scrollViewToRowIn(AlignFrame alf, String topRow)\r
+  {\r
+    try {\r
+      alf.scrollToRow(new Integer(topRow).intValue());\r
+      \r
+    } catch (Exception ex)\r
+    {\r
+      System.err.println("Couldn't parse integer arguments (topRow='"+topRow+"')");\r
       ex.printStackTrace();\r
     }\r
   }\r
 \r
+  /* (non-Javadoc)\r
+   * @see jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui.AlignFrame, java.lang.String)\r
+   */\r
+  @Override\r
+  public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)\r
+  {\r
+\r
+    try {\r
+      alf.scrollToColumn(new Integer(leftHandColumn).intValue());\r
+      \r
+    } catch (Exception ex)\r
+    {\r
+      System.err.println("Couldn't parse integer arguments (leftHandColumn='"+leftHandColumn+"')");\r
+      ex.printStackTrace();\r
+    } \r
+  }\r
+\r
   // //////////////////////////////////////////////\r
   // //////////////////////////////////////////////\r
 \r

diff --git a/src/jalview/javascript/JalviewLiteJsApi.java b/src/jalview/javascript/JalviewLiteJsApi.java
index a7255b0..19b74ca 100644 (file)
--- a/src/jalview/javascript/JalviewLiteJsApi.java
+++ b/src/jalview/javascript/JalviewLiteJsApi.java
@@ -400,7 +400,7 @@ public interface JalviewLiteJsApi
           String pdbEntryString, String pdbFile);
 
   /**
-   * adjust horizontal/vertical scroll to the make the given location the top left hand corner for given current view
+   * adjust horizontal/vertical scroll to make the given location the top left hand corner for the given view
    * 
    * @param alf
    * @param topRow
@@ -408,6 +408,20 @@ public interface JalviewLiteJsApi
    */
   public abstract void scrollViewToIn(AlignFrame alf, String topRow,
           String leftHandColumn);
+  /**
+   * adjust vertical scroll to make the given row the top one for given view
+   * 
+   * @param alf
+   * @param topRow
+   */
+  public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
+  /**
+   * adjust horizontal scroll to make the given column the left one in the given view
+   * 
+   * @param alf
+   * @param leftHandColumn
+   */
+  public abstract void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn);
 
   /**
    *