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JAL-2814 help links from PDB and Uniprot FTS panels
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 21 May 2018 09:36:35 +0000
(10:36 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 21 May 2018 09:36:35 +0000
(10:36 +0100)
help/help.jhm
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|
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help/html/features/pdbsequencefetcher.html
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|
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help/html/features/uniprotsequencefetcher.html
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src/jalview/fts/core/GFTSPanel.java
patch
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src/jalview/fts/service/pdb/PDBFTSPanel.java
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history
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
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history
src/jalview/gui/Help.java
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diff --git
a/help/help.jhm
b/help/help.jhm
index
d9a201a
..
a8ff7fa
100755
(executable)
--- a/
help/help.jhm
+++ b/
help/help.jhm
@@
-145,6
+145,7
@@
<mapID target="biojson" url="html/features/bioJsonFormat.html" />
<mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
<mapID target="biojson" url="html/features/bioJsonFormat.html" />
<mapID target="pdbfetcher" url="html/features/pdbsequencefetcher.html" />
+ <mapID target="pdbfts" url="html/features/pdbsequencefetcher.html#pdbfts" />
<mapID target="siftsmapping" url="html/features/siftsmapping.html" />
<mapID target="pdbchooser" url="html/features/structurechooser.html" />
<mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
<mapID target="siftsmapping" url="html/features/siftsmapping.html" />
<mapID target="pdbchooser" url="html/features/structurechooser.html" />
<mapID target="selectcolbyannot" url="html/features/columnFilterByAnnotation.html" />
@@
-153,6
+154,7
@@
<mapID target="ensemblfetch" url="html/features/ensemblsequencefetcher.html" />
<mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
<mapID target="ensemblfetch" url="html/features/ensemblsequencefetcher.html" />
<mapID target="uniprotfetcher" url="html/features/uniprotsequencefetcher.html" />
+ <mapID target="uniprotfts" url="html/features/uniprotsequencefetcher.html#uniprotfts" />
<mapID target="urllinks" url="html/webServices/urllinks.html" />
<mapID target="linksprefs" url="html/features/preferences.html#links" />
<mapID target="urllinks" url="html/webServices/urllinks.html" />
<mapID target="linksprefs" url="html/features/preferences.html#links" />
diff --git
a/help/html/features/pdbsequencefetcher.html
b/help/html/features/pdbsequencefetcher.html
index
bb63bed
..
9251277
100644
(file)
--- a/
help/html/features/pdbsequencefetcher.html
+++ b/
help/html/features/pdbsequencefetcher.html
@@
-43,7
+43,7
@@
alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
<p>
alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
<p>
- <strong>Searching the PDB Database</strong>
+ <a name="pdbfts"><strong>Searching the PDB Database</strong></a>
</p>
<p>To search the PDB, begin typing in the text box. If the
'autosearch' checkbox is enabled, then the results of your query
</p>
<p>To search the PDB, begin typing in the text box. If the
'autosearch' checkbox is enabled, then the results of your query
diff --git
a/help/html/features/uniprotsequencefetcher.html
b/help/html/features/uniprotsequencefetcher.html
index
4a64f52
..
72e7649
100644
(file)
--- a/
help/html/features/uniprotsequencefetcher.html
+++ b/
help/html/features/uniprotsequencefetcher.html
@@
-44,7
+44,7
@@
</p>
<p>
</p>
<p>
- <strong>Searching the UniProt Database</strong>
+ <a name="uniprotfts"><strong>Searching the UniProt Database</strong></a>
</p>
<p>To search UniProt, simply begin typing in the text box. If the
'autosearch' check box is enabled, then after a short delay (about
</p>
<p>To search UniProt, simply begin typing in the text box. If the
'autosearch' check box is enabled, then after a short delay (about
diff --git
a/src/jalview/fts/core/GFTSPanel.java
b/src/jalview/fts/core/GFTSPanel.java
index
86710e1
..
232561c
100644
(file)
--- a/
src/jalview/fts/core/GFTSPanel.java
+++ b/
src/jalview/fts/core/GFTSPanel.java
@@
-34,6
+34,7
@@
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Dimension;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Dimension;
+import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
@@
-86,6
+87,8
@@
import javax.swing.text.JTextComponent;
@SuppressWarnings("serial")
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
{
@SuppressWarnings("serial")
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
{
+ private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
+
protected JInternalFrame mainFrame = new JInternalFrame(
getFTSFrameTitle());
protected JInternalFrame mainFrame = new JInternalFrame(
getFTSFrameTitle());
@@
-300,11
+303,11
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
Integer height = getTempUserPrefs().get("FTSPanel.height") == null ? 400
: getTempUserPrefs().get("FTSPanel.height");
lbl_warning.setVisible(false);
Integer height = getTempUserPrefs().get("FTSPanel.height") == null ? 400
: getTempUserPrefs().get("FTSPanel.height");
lbl_warning.setVisible(false);
- lbl_warning.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_warning.setFont(VERDANA_12);
lbl_loading.setVisible(false);
lbl_loading.setVisible(false);
- lbl_loading.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_loading.setFont(VERDANA_12);
lbl_blank.setVisible(true);
lbl_blank.setVisible(true);
- lbl_blank.setFont(new java.awt.Font("Verdana", 0, 12));
+ lbl_blank.setFont(VERDANA_12);
tbl_summary.setAutoCreateRowSorter(true);
tbl_summary.getTableHeader().setReorderingAllowed(false);
tbl_summary.setAutoCreateRowSorter(true);
tbl_summary.getTableHeader().setReorderingAllowed(false);
@@
-357,6
+360,19
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
}
});
}
});
+ JButton txt_help = new JButton("?");
+ txt_help.setFont(VERDANA_12);
+ txt_help.setPreferredSize(new Dimension(15, 15));
+ txt_help.setToolTipText(MessageManager.getString("action.help"));
+ txt_help.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHelp();
+ }
+ });
+
btn_autosearch.setText(MessageManager.getString("option.autosearch"));
btn_autosearch.setToolTipText(
MessageManager.getString("option.enable_disable_autosearch"));
btn_autosearch.setText(MessageManager.getString("option.autosearch"));
btn_autosearch.setToolTipText(
MessageManager.getString("option.enable_disable_autosearch"));
@@
-371,7
+387,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
Boolean.toString(btn_autosearch.isSelected()));
}
});
Boolean.toString(btn_autosearch.isSelected()));
}
});
- btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_back.setFont(VERDANA_12);
btn_back.setText(MessageManager.getString("action.back"));
btn_back.addActionListener(new java.awt.event.ActionListener()
{
btn_back.setText(MessageManager.getString("action.back"));
btn_back.addActionListener(new java.awt.event.ActionListener()
{
@@
-394,7
+410,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
});
btn_ok.setEnabled(false);
});
btn_ok.setEnabled(false);
- btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_ok.setFont(VERDANA_12);
btn_ok.setText(MessageManager.getString("action.ok"));
btn_ok.addActionListener(new java.awt.event.ActionListener()
{
btn_ok.setText(MessageManager.getString("action.ok"));
btn_ok.addActionListener(new java.awt.event.ActionListener()
{
@@
-418,7
+434,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
btn_next_page.setEnabled(false);
btn_next_page.setToolTipText(
MessageManager.getString("label.next_page_tooltip"));
btn_next_page.setEnabled(false);
btn_next_page.setToolTipText(
MessageManager.getString("label.next_page_tooltip"));
- btn_next_page.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_next_page.setFont(VERDANA_12);
btn_next_page.setText(MessageManager.getString("action.next_page"));
btn_next_page.addActionListener(new java.awt.event.ActionListener()
{
btn_next_page.setText(MessageManager.getString("action.next_page"));
btn_next_page.addActionListener(new java.awt.event.ActionListener()
{
@@
-443,7
+459,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
btn_prev_page.setEnabled(false);
btn_prev_page.setToolTipText(
MessageManager.getString("label.prev_page_tooltip"));
btn_prev_page.setEnabled(false);
btn_prev_page.setToolTipText(
MessageManager.getString("label.prev_page_tooltip"));
- btn_prev_page.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_prev_page.setFont(VERDANA_12);
btn_prev_page.setText(MessageManager.getString("action.prev_page"));
btn_prev_page.addActionListener(new java.awt.event.ActionListener()
{
btn_prev_page.setText(MessageManager.getString("action.prev_page"));
btn_prev_page.addActionListener(new java.awt.event.ActionListener()
{
@@
-476,7
+492,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
btn_next_page.setVisible(false);
}
btn_next_page.setVisible(false);
}
- btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_cancel.setFont(VERDANA_12);
btn_cancel.setText(MessageManager.getString("action.cancel"));
btn_cancel.addActionListener(new java.awt.event.ActionListener()
{
btn_cancel.setText(MessageManager.getString("action.cancel"));
btn_cancel.addActionListener(new java.awt.event.ActionListener()
{
@@
-499,7
+515,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
});
scrl_searchResult.setPreferredSize(new Dimension(width, height));
});
scrl_searchResult.setPreferredSize(new Dimension(width, height));
- cmb_searchTarget.setFont(new java.awt.Font("Verdana", 0, 12));
+ cmb_searchTarget.setFont(VERDANA_12);
cmb_searchTarget.addItemListener(new ItemListener()
{
@Override
cmb_searchTarget.addItemListener(new ItemListener()
{
@Override
@@
-532,7
+548,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
}
});
}
});
- txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
+ txt_search.setFont(VERDANA_12);
txt_search.getEditor().getEditorComponent()
.addKeyListener(new KeyAdapter()
txt_search.getEditor().getEditorComponent()
.addKeyListener(new KeyAdapter()
@@
-666,6
+682,7
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
pnl_results.add(tabbedPane);
pnl_inputs.add(cmb_searchTarget);
pnl_inputs.add(txt_search);
pnl_results.add(tabbedPane);
pnl_inputs.add(cmb_searchTarget);
pnl_inputs.add(txt_search);
+ pnl_inputs.add(txt_help);
pnl_inputs.add(btn_autosearch);
pnl_inputs.add(lbl_loading);
pnl_inputs.add(lbl_warning);
pnl_inputs.add(btn_autosearch);
pnl_inputs.add(lbl_loading);
pnl_inputs.add(lbl_warning);
@@
-710,6
+727,8
@@
public abstract class GFTSPanel extends JPanel implements GFTSPanelI
Desktop.addInternalFrame(mainFrame, getFTSFrameTitle(), width, height);
}
Desktop.addInternalFrame(mainFrame, getFTSFrameTitle(), width, height);
}
+ abstract protected void showHelp();
+
protected void closeAction()
{
getTempUserPrefs().put("FTSPanel.width", this.getWidth());
protected void closeAction()
{
getTempUserPrefs().put("FTSPanel.width", this.getWidth());
diff --git
a/src/jalview/fts/service/pdb/PDBFTSPanel.java
b/src/jalview/fts/service/pdb/PDBFTSPanel.java
index
053d91b
..
da164f0
100644
(file)
--- a/
src/jalview/fts/service/pdb/PDBFTSPanel.java
+++ b/
src/jalview/fts/service/pdb/PDBFTSPanel.java
@@
-26,6
+26,8
@@
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
+import jalview.gui.Help;
+import jalview.gui.Help.HelpId;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
@@
-33,13
+35,15
@@
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.HashSet;
import java.util.Map;
+import javax.help.HelpSetException;
+
@SuppressWarnings("serial")
public class PDBFTSPanel extends GFTSPanel
{
private static String defaultFTSFrameTitle = MessageManager
.getString("label.pdb_sequence_fetcher");
@SuppressWarnings("serial")
public class PDBFTSPanel extends GFTSPanel
{
private static String defaultFTSFrameTitle = MessageManager
.getString("label.pdb_sequence_fetcher");
- private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
+ private static Map<String, Integer> tempUserPrefs = new HashMap<>();
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
@@
-190,7
+194,7
@@
public class PDBFTSPanel extends GFTSPanel
// mainFrame.dispose();
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
// mainFrame.dispose();
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<String>();
+ HashSet<String> selectedIdsSet = new HashSet<>();
int primaryKeyColIndex = 0;
try
{
int primaryKeyColIndex = 0;
try
{
@@
-288,4
+292,16
@@
public class PDBFTSPanel extends GFTSPanel
{
return PDB_AUTOSEARCH;
}
{
return PDB_AUTOSEARCH;
}
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.PdbFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
}
\ No newline at end of file
}
\ No newline at end of file
diff --git
a/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
b/src/jalview/fts/service/uniprot/UniprotFTSPanel.java
index
df54dea
..
977abfa
100644
(file)
--- a/
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
+++ b/
src/jalview/fts/service/uniprot/UniprotFTSPanel.java
@@
-26,6
+26,8
@@
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
+import jalview.gui.Help;
+import jalview.gui.Help.HelpId;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
@@
-33,6
+35,8
@@
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.HashSet;
import java.util.Map;
+import javax.help.HelpSetException;
+
@SuppressWarnings("serial")
public class UniprotFTSPanel extends GFTSPanel
{
@SuppressWarnings("serial")
public class UniprotFTSPanel extends GFTSPanel
{
@@
-245,4
+249,16
@@
public class UniprotFTSPanel extends GFTSPanel
{
return UNIPROT_AUTOSEARCH;
}
{
return UNIPROT_AUTOSEARCH;
}
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.UniprotFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
}
}
diff --git
a/src/jalview/gui/Help.java
b/src/jalview/gui/Help.java
index
f2d8113
..
cba9c2c
100644
(file)
--- a/
src/jalview/gui/Help.java
+++ b/
src/jalview/gui/Help.java
@@
-28,17
+28,17
@@
import javax.help.HelpSet;
import javax.help.HelpSetException;
/**
import javax.help.HelpSetException;
/**
- * Utility class to show the help documentation window.
+ * Utility class to show the help documentation window
*
* @author gmcarstairs
*
* @author gmcarstairs
- *
*/
public class Help
{
public enum HelpId
{
Home("home"), SequenceFeatureSettings("seqfeatures.settings"),
*/
public class Help
{
public enum HelpId
{
Home("home"), SequenceFeatureSettings("seqfeatures.settings"),
- StructureViewer("viewingpdbs");
+ StructureViewer("viewingpdbs"), PdbFts("pdbfts"),
+ UniprotFts("uniprotfts");
private String id;
private String id;