Author: scooter
Date: 2011-01-13 17:41:48 -0800 (Thu, 13 Jan 2011)
New Revision: 23452
Modified:
csplugins/trunk/ucsf/scooter/structureViz/resources/plugin.props
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/ListenerThreads.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ActionPopupMenu.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
Log:
1.9 release complete.
Modified: csplugins/trunk/ucsf/scooter/structureViz/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/structureViz/resources/plugin.props
2011-01-13 23:53:33 UTC (rev 23451)
+++ csplugins/trunk/ucsf/scooter/structureViz/resources/plugin.props
2011-01-14 01:41:48 UTC (rev 23452)
@@ -31,4 +31,4 @@
pluginAuthorsIntsitutions=John "Scooter" Morris:UCSF
# Date this plugin/plugin version was released
-releaseDate=December 28, 2010
+releaseDate=January 15, 2011
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/ListenerThreads.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/ListenerThreads.java
2011-01-13 23:53:33 UTC (rev 23451)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/actions/ListenerThreads.java
2011-01-14 01:41:48 UTC (rev 23452)
@@ -154,7 +154,7 @@
synchronized (replyLog) {
while ((line = lineReader.readLine()) != null) {
- // System.out.println("From Chimera (CMD)
-->"+line);
+ // System.out.println("From Chimera
("+command+") -->"+line);
if (line.startsWith("CMD")) {
logger.error("Got unexpected command
from Chimera: "+line);
@@ -189,6 +189,7 @@
public ModelUpdater() {}
public void run() {
+ // System.out.println("Model updated");
chimeraObject.refresh();
chimeraObject.modelChanged();
// Now update our selection from Chimera
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ActionPopupMenu.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ActionPopupMenu.java
2011-01-13 23:53:33 UTC (rev 23451)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ActionPopupMenu.java
2011-01-14 01:41:48 UTC (rev 23452)
@@ -126,9 +126,7 @@
{
addItem(submenu, "All", "disp %sel",0);
addItem(submenu, "Backbone only", "~disp %sel; disp
%sel & @n,ca,c",0);
- if (modelList.size() > 0 || chainList.size() > 0) {
- addItem(submenu, "Sequence", "sequence %sel",0);
- }
+ addItem(submenu, "Sequence", "sequence %sel",0);
}
add(submenu);
// Hide
@@ -219,12 +217,12 @@
addItem(selectMenu, "Ligand", "select %sel & ligand",
PopupActionListener.MODEL_SELECTION);
addItem(selectMenu, "Ions", "select %sel & ions",
PopupActionListener.MODEL_SELECTION);
addItem(selectMenu, "Solvent", "select %sel & solvent",
PopupActionListener.MODEL_SELECTION);
- addItem(selectMenu, "Functional Residues", null,
PopupActionListener.FUNCTIONAL_RESIDUES);
JMenu secondaryMenu = new JMenu("Secondary Structure");
addItem(secondaryMenu, "Helix", "select %sel & helix",
PopupActionListener.MODEL_SELECTION);
addItem(secondaryMenu, "Strand", "select %sel & strand",
PopupActionListener.MODEL_SELECTION);
addItem(secondaryMenu, "Coil", "select %sel & coil",
PopupActionListener.MODEL_SELECTION);
selectMenu.add(secondaryMenu);
+ addItem(selectMenu, "Functional Residues", null,
PopupActionListener.FUNCTIONAL_RESIDUES);
add(selectMenu);
return;
}
@@ -307,8 +305,9 @@
JMenu colorMenu = new JMenu(text);
JMenuItem colorItem;
if (addByElement) {
- addItem(colorMenu, "By element", "color byelement
%sel",0);
- addItem(colorMenu, "By heteroatom", "color byhetero
%sel",0);
+ addItem(colorMenu, "By element", "color byelement
%sel,a",0);
+ // addItem(colorMenu, "By heteroatom", "color byhetero
%sel",0);
+ addItem(colorMenu, "By heteroatom", "~color %sel,a;
color byhetero %sel,a",0);
}
for (int color=0; color < colorList.length; color++) {
colorItem = addItem(colorMenu, colorList[color],
prefix+colorList[color]+suffix,0);
@@ -465,7 +464,7 @@
chimeraObject.chimeraSend(commandList[i]);
}
if (postCommand == CLEAR_SELECTION) {
- navTree.clearSelection();
+
navTree.removeSelectionPaths(navTree.getSelectionPaths());
} else if (postCommand == CLOSE) {
// Get the object
for (ChimeraStructuralObject obj: objectList) {
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-01-13 23:53:33 UTC (rev 23451)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/ModelNavigatorDialog.java
2011-01-14 01:41:48 UTC (rev 23452)
@@ -93,6 +93,8 @@
private static final int FINDHBOND = 17;
private static final int FUNCTIONALRESIDUES = 18;
private static final int COLLAPSEALL = 19;
+ private static final int EXPANDMODELS = 20;
+ private static final int EXPANDCHAINS = 21;
private boolean ignoreSelection = false;
private int residueDisplay = ChimeraResidue.THREE_LETTER;
private boolean isCollapsing = false;
@@ -308,16 +310,13 @@
*/
public void updateSelection(List<ChimeraStructuralObject>
selectionList) {
// System.out.println("Model Navigator Panel: updateSelection
("+selectionList+")");
- TreePath path = null;
+ List<TreePath> pathList = new ArrayList<TreePath>();
this.ignoreSelection = true;
- // Need to clear currently selected objects
- clearSelectionState();
- navigationTree.clearSelection();
for (ChimeraStructuralObject selectedObject: selectionList) {
- path = (TreePath)selectedObject.getUserData();
- navigationTree.addSelectionPath(path);
- navigationTree.makeVisible(path);
+ pathList.add((TreePath)selectedObject.getUserData());
}
+ // Need to clear currently selected objects
+ resetSelectionState(pathList);
int row = navigationTree.getMaxSelectionRow();
navigationTree.scrollRowToVisible(row);
this.ignoreSelection = false;
@@ -329,7 +328,8 @@
* iterating over all models and recursively decending
* through the chains to the residues.
*/
- private void clearSelectionState() {
+ private void resetSelectionState(List<TreePath> setPaths) {
+
navigationTree.removeSelectionPaths(navigationTree.getSelectionPaths());
List<ChimeraModel>models = chimeraObject.getChimeraModels();
if (models == null) return;
for (ChimeraModel m: models) {
@@ -341,10 +341,15 @@
Collection<ChimeraResidue>residues =
c.getResidues();
if (residues == null ) continue;
for (ChimeraResidue r: residues) {
- if (r != null) r.setSelected(false);
+ if (r != null) {
+ r.setSelected(false);
+ }
}
}
}
+ // navigationTree.removeSelectionPaths(clearPaths.toArray(new
TreePath[1]));
+ if (setPaths != null && setPaths.size() > 0)
+ navigationTree.addSelectionPaths(setPaths.toArray(new
TreePath[1]));
}
/**
@@ -436,13 +441,13 @@
// View menu
JMenu viewMenu = new JMenu("View");
- // addMenuItem(viewMenu, "Collapse Model Tree", COLLAPSEALL,
null);
- // addMenuItem(viewMenu, "Expand Models", COLLAPSEALL, null);
- // addMenuItem(viewMenu, "Expand Chains", COLLAPSEALL, null);
+ addMenuItem(viewMenu, "Collapse model tree", COLLAPSEALL, null);
+ addMenuItem(viewMenu, "Expand all models", EXPANDMODELS, null);
+ addMenuItem(viewMenu, "Expand all chains", EXPANDCHAINS, null);
addMenuItem(viewMenu, "Refresh model tree", REFRESH, null);
- JMenu viewResidues = new JMenu("Residues as..");
+ JMenu viewResidues = new JMenu("Show residues as..");
addMenuItem(viewResidues, "single letter",
ChimeraResidue.SINGLE_LETTER, null);
addMenuItem(viewResidues, "three letters",
@@ -540,6 +545,37 @@
return true;
}
+ private void collapseAll() {
+ int row = navigationTree.getRowCount() - 1;
+ while (row >= 1) {
+ navigationTree.collapseRow(row);
+ row--;
+ }
+ return;
+ }
+
+ private void expandModels() {
+ expandTree(2);
+ return;
+ }
+
+ private void expandChains() {
+ expandTree(3);
+ return;
+ }
+
+ private void expandTree(int depth) {
+ int row = navigationTree.getRowCount() - 1;
+ while (row >= 1) {
+ TreePath path = navigationTree.getPathForRow(row);
+ Object[] objArray = path.getPath();
+ if (objArray.length == depth)
+ navigationTree.expandRow(row);
+ row--;
+ }
+ return;
+ }
+
// Embedded classes
/**
@@ -576,14 +612,12 @@
chimeraObject.select(command);
} else if (type == CLEAR) {
chimeraObject.select("~select");
- navigationTree.clearSelection();
- clearSelectionState();
+
navigationTree.removeSelectionPaths(navigationTree.getSelectionPaths());
} else if (type == EXIT) {
chimeraObject.exit();
setVisible(false);
if (chimeraObject.getAlignDialog() != null)
chimeraObject.getAlignDialog().setVisible(false);
- return;
} else if (type == FUNCTIONALRESIDUES) {
String command = null;
// For all open structures, select the
functional residues
@@ -596,6 +630,8 @@
for (String residue: residueL) {
residues =
residues.concat(residue+",");
}
+ if (residues.length() == 0)
+ return;
residues =
residues.substring(0,residues.length()-1);
if (command == null)
command = "select
#"+structure.modelNumber()+":"+residues;
@@ -607,17 +643,18 @@
} else if (type == REFRESH) {
chimeraObject.refresh();
} else if (type == COLLAPSEALL) {
- // TODO: for some reason, this doesn't work!
- int row = navigationTree.getRowCount() - 1;
- while (row >= 1) {
- navigationTree.collapseRow(row);
- row--;
- }
- navigationTree.treeDidChange();
+ collapseAll();
+ } else if (type == EXPANDMODELS) {
+ expandModels();
+ } else if (type == EXPANDCHAINS) {
+ expandModels();
+ expandChains();
} else if (type == ALIGNBYMODEL) {
launchAlignDialog(false);
+ chimeraObject.modelChanged();
} else if (type == ALIGNBYCHAIN) {
launchAlignDialog(true);
+ chimeraObject.modelChanged();
} else if (type == FINDCLASH) {
if (selectedObjects.size() > 0) {
chimeraObject.select(command);
@@ -635,8 +672,8 @@
} else {
residueDisplay = type;
treeModel.setResidueDisplay(type);
+ chimeraObject.modelChanged();
}
- modelChanged();
}
/**
Modified:
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
2011-01-13 23:53:33 UTC (rev 23451)
+++
csplugins/trunk/ucsf/scooter/structureViz/src/structureViz/ui/StructureVizMenuHandler.java
2011-01-14 01:41:48 UTC (rev 23452)
@@ -148,8 +148,8 @@
}
/**
- * Search modbase for modelled structures that correspond to this
identifier.
- * Since modelled structures can be somewhat misleading, popup a
warning dialog
+ * Search modbase for modeled structures that correspond to this
identifier.
+ * Since modeled structures can be somewhat misleading, popup a warning
dialog
* while we do the fetch.
*/
private void findModelsAction() {
@@ -160,7 +160,7 @@
if (showModelWarning) {
SwingUtilities.invokeLater(new Runnable() {
public void run() {
- String message = "<html><b>Warning</b>:
Modelled structures are predictions, not experimental data.<br>";
+ String message = "<html><b>Warning</b>:
Modeled structures are predictions, not experimental data.<br>";
message += "These structures are from
the ModBase web service at <a
href=\"http://modbase.salilab.org\";>http://modbase.salilab.org/</a><br>";
message += "Measures of model
reliability, or likelihood of correctness, are provided in the<br>";
message += "Chimera ModBase Model
List.</html>";
@@ -176,7 +176,7 @@
JOptionPane.DEFAULT_OPTION,
null,
options);
- JDialog jd =
dialog.createDialog(chimera.getDialog(), "Modelled Structure Warning");
+ JDialog jd =
dialog.createDialog(chimera.getDialog(), "Modeled Structure Warning");
jd.pack();
jd.setVisible(true);
}
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