git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
9f55824
)
JAL-3048 TODOs for refactoring JalviewFileChooser pattern
author
Jim Procter
<jprocter@issues.jalview.org>
Thu, 28 Jun 2018 15:51:32 +0000
(16:51 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Thu, 28 Jun 2018 15:52:08 +0000
(16:52 +0100)
13 files changed:
src/jalview/gui/AlignFrame.java
patch
|
blob
|
history
src/jalview/gui/AnnotationExporter.java
patch
|
blob
|
history
src/jalview/gui/CutAndPasteHtmlTransfer.java
patch
|
blob
|
history
src/jalview/gui/CutAndPasteTransfer.java
patch
|
blob
|
history
src/jalview/gui/Desktop.java
patch
|
blob
|
history
src/jalview/gui/FeatureSettings.java
patch
|
blob
|
history
src/jalview/gui/StructureChooser.java
patch
|
blob
|
history
src/jalview/gui/StructureViewerBase.java
patch
|
blob
|
history
src/jalview/gui/TreePanel.java
patch
|
blob
|
history
src/jalview/gui/UserDefinedColours.java
patch
|
blob
|
history
src/jalview/gui/WsParamSetManager.java
patch
|
blob
|
history
src/jalview/io/HTMLOutput.java
patch
|
blob
|
history
src/jalview/util/ImageMaker.java
patch
|
blob
|
history
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
a40044a
..
aa0a1fe
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-1118,6
+1118,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void saveAs_actionPerformed(ActionEvent e)
{
@Override
public void saveAs_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 JalviewFileChooser - Save option
+
String format = currentFileFormat == null ? null
: currentFileFormat.getName();
JalviewFileChooser chooser = JalviewFileChooser
String format = currentFileFormat == null ? null
: currentFileFormat.getName();
JalviewFileChooser chooser = JalviewFileChooser
@@
-1422,7
+1424,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void associatedData_actionPerformed(ActionEvent e)
{
@Override
public void associatedData_actionPerformed(ActionEvent e)
{
- // Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
@@
-3904,6
+3905,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 JalviewFileChooser
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
@@
-4550,7
+4552,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
for (Object[] o : filesmatched)
{
*/
for (Object[] o : filesmatched)
{
- filesnotmatched.add((String) o[0]);
+ filesnotmatched.add(o[0]);
}
}
}
}
}
}
diff --git
a/src/jalview/gui/AnnotationExporter.java
b/src/jalview/gui/AnnotationExporter.java
index
6fefbd0
..
35a463c
100644
(file)
--- a/
src/jalview/gui/AnnotationExporter.java
+++ b/
src/jalview/gui/AnnotationExporter.java
@@
-135,6
+135,7
@@
public class AnnotationExporter extends JPanel
private void toFile_actionPerformed()
{
private void toFile_actionPerformed()
{
+ // TODO: JAL-3048 JalviewFileChooser - Save option
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
diff --git
a/src/jalview/gui/CutAndPasteHtmlTransfer.java
b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index
2e51bce
..
03eb7d2
100644
(file)
--- a/
src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/
src/jalview/gui/CutAndPasteHtmlTransfer.java
@@
-148,6
+148,8
@@
public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
@Override
public void save_actionPerformed(ActionEvent e)
{
@Override
public void save_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 JalviewFileChooser - Save option
+
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
diff --git
a/src/jalview/gui/CutAndPasteTransfer.java
b/src/jalview/gui/CutAndPasteTransfer.java
index
2a96daf
..
142dd75
100644
(file)
--- a/
src/jalview/gui/CutAndPasteTransfer.java
+++ b/
src/jalview/gui/CutAndPasteTransfer.java
@@
-135,6
+135,8
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
@Override
public void save_actionPerformed(ActionEvent e)
{
@Override
public void save_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 JalviewFileChooser - Save option
+
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
diff --git
a/src/jalview/gui/Desktop.java
b/src/jalview/gui/Desktop.java
index
39098f2
..
61d2b11
100644
(file)
--- a/
src/jalview/gui/Desktop.java
+++ b/
src/jalview/gui/Desktop.java
@@
-1613,6
+1613,8
@@
public class Desktop extends jalview.jbgui.GDesktop
@Override
public void saveState_actionPerformed(ActionEvent e)
{
@Override
public void saveState_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 not needed for Jalview-JS
+
JalviewFileChooser chooser = new JalviewFileChooser("jvp",
"Jalview Project");
JalviewFileChooser chooser = new JalviewFileChooser("jvp",
"Jalview Project");
@@
-1686,6
+1688,8
@@
public class Desktop extends jalview.jbgui.GDesktop
@Override
public void loadState_actionPerformed(ActionEvent e)
{
@Override
public void loadState_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 not needed for Jalview-JS
+
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "jvp", "jar" },
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "jvp", "jar" },
@@
-1993,6
+1997,8
@@
public class Desktop extends jalview.jbgui.GDesktop
@Override
public void vamsasImport_actionPerformed(ActionEvent e)
{
@Override
public void vamsasImport_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 not needed for Jalview-JS
+
if (v_client == null)
{
// Load and try to start a session.
if (v_client == null)
{
// Load and try to start a session.
@@
-2269,6
+2275,8
@@
public class Desktop extends jalview.jbgui.GDesktop
@Override
public void vamsasSave_actionPerformed(ActionEvent e)
{
@Override
public void vamsasSave_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 not needed for Jalview-JS
+
if (v_client != null)
{
// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
if (v_client != null)
{
// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
diff --git
a/src/jalview/gui/FeatureSettings.java
b/src/jalview/gui/FeatureSettings.java
index
78c1cac
..
75e8ec9
100644
(file)
--- a/
src/jalview/gui/FeatureSettings.java
+++ b/
src/jalview/gui/FeatureSettings.java
@@
-846,6
+846,9
@@
public class FeatureSettings extends JPanel
*/
void load()
{
*/
void load()
{
+ // TODO: JAL-3048 relies on Castor XML parsing: not needed for JS-jalview core
+ // functionalty
+
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
@@
-928,6
+931,7
@@
public class FeatureSettings extends JPanel
*/
void save()
{
*/
void save()
{
+ // TODO: JAL-3048 not needed for Jalview-JS - save colours
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
diff --git
a/src/jalview/gui/StructureChooser.java
b/src/jalview/gui/StructureChooser.java
index
e18d6af
..
97ff404
100644
(file)
--- a/
src/jalview/gui/StructureChooser.java
+++ b/
src/jalview/gui/StructureChooser.java
@@
-565,6
+565,8
@@
public class StructureChooser extends GStructureChooser
@Override
protected void pdbFromFile_actionPerformed()
{
@Override
protected void pdbFromFile_actionPerformed()
{
+ // TODO: JAL-3048 not needed for Jalview-JS until JSmol dep and StructureChooser
+ // works
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
diff --git
a/src/jalview/gui/StructureViewerBase.java
b/src/jalview/gui/StructureViewerBase.java
index
72b0bcc
..
9ed08b8
100644
(file)
--- a/
src/jalview/gui/StructureViewerBase.java
+++ b/
src/jalview/gui/StructureViewerBase.java
@@
-876,6
+876,7
@@
public abstract class StructureViewerBase extends GStructureViewer
@Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
@Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
+ // TODO: JAL-3048 not needed for Jalview-JS - save PDB file
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
diff --git
a/src/jalview/gui/TreePanel.java
b/src/jalview/gui/TreePanel.java
index
2727db1
..
5795a9f
100755
(executable)
--- a/
src/jalview/gui/TreePanel.java
+++ b/
src/jalview/gui/TreePanel.java
@@
-390,6
+390,7
@@
public class TreePanel extends GTreePanel
@Override
public void saveAsNewick_actionPerformed(ActionEvent e)
{
@Override
public void saveAsNewick_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 save newick file for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
@@
-696,6
+697,7
@@
public class TreePanel extends GTreePanel
try
{
try
{
+ // TODO: JAL-3048 not needed for Jalview-JS - Requires EpsGraphics2D dependency
JalviewFileChooser chooser = new JalviewFileChooser(
ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
chooser.setFileView(new JalviewFileView());
JalviewFileChooser chooser = new JalviewFileChooser(
ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
chooser.setFileView(new JalviewFileView());
@@
-739,6
+741,7
@@
public class TreePanel extends GTreePanel
@Override
public void pngTree_actionPerformed(ActionEvent e)
{
@Override
public void pngTree_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 image export supported in JalviewJS ?
int width = treeCanvas.getWidth();
int height = treeCanvas.getHeight();
int width = treeCanvas.getWidth();
int height = treeCanvas.getHeight();
diff --git
a/src/jalview/gui/UserDefinedColours.java
b/src/jalview/gui/UserDefinedColours.java
index
3290500
..
89ddf87
100755
(executable)
--- a/
src/jalview/gui/UserDefinedColours.java
+++ b/
src/jalview/gui/UserDefinedColours.java
@@
-633,7
+633,7
@@
public class UserDefinedColours extends GUserDefinedColours
{
upperCaseButtons = new ArrayList<>();
lowerCaseButtons = new ArrayList<>();
{
upperCaseButtons = new ArrayList<>();
lowerCaseButtons = new ArrayList<>();
-
+ // TODO: JAL-3048 requires Castor dependency for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser("jc",
"Jalview User Colours");
chooser.setFileView(new JalviewFileView());
JalviewFileChooser chooser = new JalviewFileChooser("jc",
"Jalview User Colours");
chooser.setFileView(new JalviewFileView());
@@
-754,6
+754,8
@@
public class UserDefinedColours extends GUserDefinedColours
return false;
}
}
return false;
}
}
+ // TODO: JAL-3048 saveas, also requires Castor dependency for Jalview-JS
+
JalviewFileChooser chooser = new JalviewFileChooser("jc",
"Jalview User Colours");
JalviewFileChooser chooser = new JalviewFileChooser("jc",
"Jalview User Colours");
diff --git
a/src/jalview/gui/WsParamSetManager.java
b/src/jalview/gui/WsParamSetManager.java
index
d91775c
..
a826503
100644
(file)
--- a/
src/jalview/gui/WsParamSetManager.java
+++ b/
src/jalview/gui/WsParamSetManager.java
@@
-180,6
+180,8
@@
public class WsParamSetManager implements ParamManager
}
if (filename == null)
{
}
if (filename == null)
{
+ // TODO: JAL-3048 webservice - not required for Jalview-JS
+
JalviewFileChooser chooser = new JalviewFileChooser("wsparams",
"Web Service Parameter File");
chooser.setFileView(new JalviewFileView());
JalviewFileChooser chooser = new JalviewFileChooser("wsparams",
"Web Service Parameter File");
chooser.setFileView(new JalviewFileView());
diff --git
a/src/jalview/io/HTMLOutput.java
b/src/jalview/io/HTMLOutput.java
index
bebfd28
..
bf8c431
100644
(file)
--- a/
src/jalview/io/HTMLOutput.java
+++ b/
src/jalview/io/HTMLOutput.java
@@
-228,6
+228,8
@@
public abstract class HTMLOutput implements Runnable
pSessionId);
}
pSessionId);
}
+ // TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or
+ // Jalview HTML rendering system- probably not required for Jalview-JS)
JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
"HTML files");
jvFileChooser.setFileView(new JalviewFileView());
JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
"HTML files");
jvFileChooser.setFileView(new JalviewFileView());
diff --git
a/src/jalview/util/ImageMaker.java
b/src/jalview/util/ImageMaker.java
index
7840261
..
3398fea
100755
(executable)
--- a/
src/jalview/util/ImageMaker.java
+++ b/
src/jalview/util/ImageMaker.java
@@
-123,6
+123,8
@@
public class ImageMaker
this.headless = headless;
if (file == null)
{
this.headless = headless;
if (file == null)
{
+ // TODO: JAL-3048 export SVG/EPS/PNG- not required for Jalview-JS
+
setProgressMessage(MessageManager.formatMessage(
"status.waiting_for_user_to_select_output_file", type.name));
JalviewFileChooser chooser;
setProgressMessage(MessageManager.formatMessage(
"status.waiting_for_user_to_select_output_file", type.name));
JalviewFileChooser chooser;