From ff303328d18feb9948a816ff95aa86bc724b0570 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 3 Aug 2004 16:31:53 +0000
Subject: [PATCH] -R
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1763 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/editor/Annotation.java | 59 ++++++++++---
uk/ac/sanger/artemis/editor/BigPane.java | 7 +-
.../artemis/editor/DataCollectionPane.java | 87 +++++++++++++------
.../artemis/editor/DataViewInternalFrame.java | 21 +++--
.../sanger/artemis/editor/FastaTextPane.java | 68 ++++++++++++++-
uk/ac/sanger/artemis/editor/HitInfo.java | 80 ++++++++++++++++-
6 files changed, 270 insertions(+), 52 deletions(-)
diff --git a/uk/ac/sanger/artemis/editor/Annotation.java b/uk/ac/sanger/artemis/editor/Annotation.java
index 6d7978d25..d0c8bb3f7 100644
--- a/uk/ac/sanger/artemis/editor/Annotation.java
+++ b/uk/ac/sanger/artemis/editor/Annotation.java
@@ -24,7 +24,9 @@
package uk.ac.sanger.artemis.editor;
+
import java.util.StringTokenizer;
+import javax.swing.border.*;
import javax.swing.event.*;
import javax.swing.text.html.*;
import javax.swing.text.DefaultStyledDocument;
@@ -248,6 +250,29 @@ public class Annotation extends JEditorPane
}
+ protected void setUpSRSFrame(URL url, String search)
+ throws IOException
+ {
+ if(BigPane.srsFrame == null)
+ {
+ BigPane.setUpSRSFrame((2*desktop.getHeight())/3,desktop);
+ Border loweredbevel = BorderFactory.createLoweredBevelBorder();
+ Border raisedbevel = BorderFactory.createRaisedBevelBorder();
+ Border compound = BorderFactory.createCompoundBorder(raisedbevel,loweredbevel);
+
+ JTextField statusField = new JTextField();
+ statusField.setBorder(compound);
+ statusField.setEditable(false);
+ BigPane.srsFrame.getContentPane().add(statusField, BorderLayout.SOUTH);
+ }
+
+ Annotation edPane = new Annotation(url);
+ JScrollPane jsp = new JScrollPane(edPane);
+ JTabbedPane jtab = (JTabbedPane)BigPane.srsFrame.getContentPane().getComponent(0);
+ jtab.insertTab(search, null,jsp,null,0);
+ BigPane.srsFrame.setVisible(true);
+ }
+
/**
*
* Method to handle hyper link events.
@@ -256,7 +281,7 @@ public class Annotation extends JEditorPane
*/
public void hyperlinkUpdate(HyperlinkEvent event)
{
- if (event.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
+ if(event.getEventType() == HyperlinkEvent.EventType.ACTIVATED)
{
setCursor(cbusy);
try
@@ -273,15 +298,7 @@ public class Annotation extends JEditorPane
if(desktop != null)
{
if(BigPane.srsTabPane.isSelected())
- {
- if(BigPane.srsFrame == null)
- BigPane.setUpSRSFrame((2*desktop.getHeight())/3,desktop);
- Annotation edPane = new Annotation(url);
- JScrollPane jsp = new JScrollPane(edPane);
- JTabbedPane jtab = (JTabbedPane)BigPane.srsFrame.getContentPane().getComponent(0);
- jtab.insertTab(search, null,jsp,null,0);
- BigPane.srsFrame.setVisible(true);
- }
+ setUpSRSFrame(url,search);
if(BigPane.srsWin.isSelected())
{
@@ -315,12 +332,34 @@ public class Annotation extends JEditorPane
{
setCursor(cdone);
ioe.printStackTrace();
+
// ("Can't follow link to " +
// event.getURL().toExternalForm() );
}
setCursor(cdone);
}
+ else if(event.getEventType() == HyperlinkEvent.EventType.ENTERED)
+ {
+ try
+ {
+ JTextField statusField = (JTextField)BigPane.srsFrame.getContentPane().getComponent(1);
+ statusField.setText(event.getDescription());
+ }
+ catch(Exception exp){}
+
+ }
+ else if(event.getEventType() == HyperlinkEvent.EventType.EXITED)
+ {
+ try
+ {
+ JTextField statusField = (JTextField)BigPane.srsFrame.getContentPane().getComponent(1);
+ statusField.setText("");
+ }
+ catch(Exception exp){}
+
+ }
+
}
diff --git a/uk/ac/sanger/artemis/editor/BigPane.java b/uk/ac/sanger/artemis/editor/BigPane.java
index 4928ae894..c47fc874c 100644
--- a/uk/ac/sanger/artemis/editor/BigPane.java
+++ b/uk/ac/sanger/artemis/editor/BigPane.java
@@ -102,8 +102,8 @@ public class BigPane extends JFrame
JMenu srsMenu = new JMenu("Show SRS in");
optionMenu.add(srsMenu);
- srsBrowser = new JCheckBoxMenuItem("External Broser",false);
- srsTabPane = new JCheckBoxMenuItem("Tabbed Pane",true);
+ srsBrowser = new JCheckBoxMenuItem("Browser",false);
+ srsTabPane = new JCheckBoxMenuItem("Tab Pane",true);
srsWin = new JCheckBoxMenuItem("New Window",false);
srsMenu.add(srsBrowser);
@@ -165,7 +165,8 @@ public class BigPane extends JFrame
public void actionPerformed(ActionEvent e)
{
int select = jtab.getSelectedIndex();
- jtab.removeTabAt(select);
+ if(select > -1)
+ jtab.removeTabAt(select);
}
});
diff --git a/uk/ac/sanger/artemis/editor/DataCollectionPane.java b/uk/ac/sanger/artemis/editor/DataCollectionPane.java
index f91b942c1..d17cd0090 100644
--- a/uk/ac/sanger/artemis/editor/DataCollectionPane.java
+++ b/uk/ac/sanger/artemis/editor/DataCollectionPane.java
@@ -25,6 +25,7 @@
package uk.ac.sanger.artemis.editor;
import javax.swing.*;
+import javax.swing.border.Border;
import java.util.StringTokenizer;
import java.io.BufferedReader;
@@ -47,7 +48,7 @@ import java.util.Hashtable;
public class DataCollectionPane extends JScrollPane
{
- public DataCollectionPane(Vector hitInfoCollection, String dataFile,
+ public DataCollectionPane(String dataFile,
final FastaTextPane fastaTextPane,
final Annotation ann, final JDesktopPane desktop)
{
@@ -60,6 +61,8 @@ public class DataCollectionPane extends JScrollPane
scrollPanel.add(bdown);
Hashtable goHash = new Hashtable();
+ Vector hitInfoCollection = fastaTextPane.getHitCollection();
+
Enumeration hitEnum = hitInfoCollection.elements();
while(hitEnum.hasMoreElements())
{
@@ -190,34 +193,9 @@ public class DataCollectionPane extends JScrollPane
try
{
URL url = new URL("http://"+srscmd);
- if(BigPane.srsTabPane.isSelected())
- {
- if(BigPane.srsFrame == null)
- {
- BigPane.setUpSRSFrame((2*desktop.getHeight())/3,desktop);
-// int hgt = (2*desktop.getHeight())/3;
-// BigPane.srsFrame = new JInternalFrame("SRS",
-// true, //resizable
-// true, //closable
-// true, //maximizable
-// true);//iconifiable
-// JTabbedPane jtab = new JTabbedPane();
-// BigPane.srsFrame.getContentPane().add(jtab);
-// BigPane.srsFrame.setLocation(0,0);
-// BigPane.srsFrame.setSize(800,hgt);
-
-// JMenuBar menuBar = new JMenuBar();
-// menuBar.add(new CommonMenu(BigPane.srsFrame));
-// BigPane.srsFrame.setJMenuBar(menuBar);
-// desktop.add(BigPane.srsFrame);
- }
- Annotation edPane = new Annotation(url);
- JScrollPane jsp = new JScrollPane(edPane);
- JTabbedPane jtab = (JTabbedPane)BigPane.srsFrame.getContentPane().getComponent(0);
- jtab.insertTab(search,null,jsp,null,0);
- BigPane.srsFrame.setVisible(true);
- }
+ if(BigPane.srsTabPane.isSelected())
+ setUpSRSFrame(url,search,desktop);
if(BigPane.srsWin.isSelected())
{
@@ -239,6 +217,14 @@ public class DataCollectionPane extends JScrollPane
desktop.add(jif);
}
}
+ catch(java.net.ConnectException connect)
+ {
+ JOptionPane.showMessageDialog(DataCollectionPane.this,
+ "Cannot retrieve "+search+
+ "\nConnection failed to:\nhttp://"+srscmd,
+ "Connection Error",
+ JOptionPane.WARNING_MESSAGE);
+ }
catch(Exception exp)
{
exp.printStackTrace();
@@ -275,6 +261,27 @@ public class DataCollectionPane extends JScrollPane
{
String go_cmd = "http://www.godatabase.org/cgi-bin/amigo/go.cgi?query=GO%3A"+go_id;
BrowserControl.displayURL(go_cmd);
+
+ if(BigPane.srsTabPane.isSelected())
+ {
+ try
+ {
+ setUpSRSFrame(new URL(go_cmd),go_id,desktop);
+ }
+ catch(java.net.ConnectException connect)
+ {
+ JOptionPane.showMessageDialog(DataCollectionPane.this,
+ "Cannot retrieve "+go_id+
+ "\nConnection failed to:\n"+go_cmd,
+ "Connection Error",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ catch(Exception exp)
+ {
+ exp.printStackTrace();
+ }
+ }
+
}
});
bacross.add(Box.createHorizontalStrut(10));
@@ -295,6 +302,30 @@ public class DataCollectionPane extends JScrollPane
}
+ protected void setUpSRSFrame(URL url, String search, JDesktopPane desktop)
+ throws IOException
+ {
+ if(BigPane.srsFrame == null)
+ {
+ BigPane.setUpSRSFrame((2*desktop.getHeight())/3,desktop);
+ Border loweredbevel = BorderFactory.createLoweredBevelBorder();
+ Border raisedbevel = BorderFactory.createRaisedBevelBorder();
+ Border compound = BorderFactory.createCompoundBorder(raisedbevel,loweredbevel);
+
+ JTextField statusField = new JTextField();
+ statusField.setBorder(compound);
+ statusField.setEditable(false);
+ BigPane.srsFrame.getContentPane().add(statusField, BorderLayout.SOUTH);
+ }
+
+ Annotation edPane = new Annotation(url);
+ JScrollPane jsp = new JScrollPane(edPane);
+ JTabbedPane jtab = (JTabbedPane)BigPane.srsFrame.getContentPane().getComponent(0);
+ jtab.insertTab(search, null,jsp,null,0);
+ BigPane.srsFrame.setVisible(true);
+ }
+
+
protected static void getzCall(HitInfo hit, boolean ortholog)
{
String env[] = { "PATH=/usr/local/pubseq/bin/" };
diff --git a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
index 90a8b5a85..665a1953f 100644
--- a/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
+++ b/uk/ac/sanger/artemis/editor/DataViewInternalFrame.java
@@ -43,8 +43,6 @@ public class DataViewInternalFrame extends JInternalFrame
true);//iconifiable
Annotation ann = new Annotation(desktop);
- JPanel dataPanel = (JPanel)getContentPane();
- dataPanel.setLayout(new BorderLayout());
StringBuffer annFormat = new StringBuffer();
@@ -56,15 +54,28 @@ public class DataViewInternalFrame extends JInternalFrame
annFormat.append("/"+fastaPane.getFormat()+"_file=\""+
dataFile[i]+"\"\n");
// add data pane
- Vector hits = fastaPane.getHitCollection();
DataCollectionPane dataPane =
- new DataCollectionPane(hits, dataFile[i], fastaPane, ann, desktop);
+ new DataCollectionPane(dataFile[i], fastaPane, ann, desktop);
JSplitPane split = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
fastaPane,dataPane);
split.setDividerLocation(150);
tabPane.add(fastaPane.getFormat(),split);
+
+ JInternalFrame jif = new JInternalFrame("Viewer",
+ true, //resizable
+ true, //closable
+ true, //maximizable
+ true);//iconifiable
+ DBViewer dbview = new DBViewer(fastaPane);
+ JScrollPane dbviewScroll = new JScrollPane(dbview);
+ dbviewScroll.setPreferredSize(new Dimension(500,200));
+ jif.getContentPane().add(dbviewScroll);
+ jif.setLocation(0,0);
+ jif.setSize(500,300);
+ jif.setVisible(true);
+ desktop.add(jif);
}
// add annotator text pane
@@ -75,7 +86,7 @@ public class DataViewInternalFrame extends JInternalFrame
JSplitPane split = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
annotationScroll,tabPane);
split.setDividerLocation(250);
- dataPanel.add(split);
+ getContentPane().add(split);
setVisible(true);
}
diff --git a/uk/ac/sanger/artemis/editor/FastaTextPane.java b/uk/ac/sanger/artemis/editor/FastaTextPane.java
index ef0e9a0d8..38c48a37a 100644
--- a/uk/ac/sanger/artemis/editor/FastaTextPane.java
+++ b/uk/ac/sanger/artemis/editor/FastaTextPane.java
@@ -155,11 +155,13 @@ public class FastaTextPane extends JScrollPane
streamReader = new InputStreamReader(getInputStream(dataFile));
buffReader = new BufferedReader(streamReader);
+ String qlen = null;
String line = null;
int textPosition = 0;
int len = 0;
HitInfo hit = null;
int ind1 = 0;
+ int endQuery = 0;
while( (line = buffReader.readLine()) != null)
{
@@ -198,6 +200,8 @@ public class FastaTextPane extends JScrollPane
hit = getHitInfo(currentID,hitInfoCollection);
hit.setStartPosition(textPosition);
+ if(qlen != null)
+ hit.setQueryLength(Integer.parseInt(qlen));
String going = "";
ind = line.indexOf("GO:");
@@ -205,18 +209,51 @@ public class FastaTextPane extends JScrollPane
going = line.substring(ind+3);
String nextLine = null;
- buffReader.mark(210);
+// buffReader.mark(210);
+
+// get GO numbers
while((nextLine = buffReader.readLine()).indexOf("Length") == -1)
{
+ len += nextLine.length()+1;
+ sbuff.append(nextLine+"\n");
if(going.equals("") && ((ind = nextLine.indexOf("GO:")) > -1))
going = nextLine.substring(ind+3);
else if(!going.equals(""))
going = going.concat(nextLine);
}
-
- buffReader.reset();
+
if(!going.equals(""))
- hit.setGO(going);
+ hit.setGO(going);
+
+ if(nextLine != null)
+ {
+ len += nextLine.length()+1;
+ sbuff.append(nextLine+"\n");
+ if( (ind1 = nextLine.indexOf(" Length = ")) > -1)
+ hit.setLength(nextLine.substring(ind1+11));
+ }
+
+// get query start
+ while(!(nextLine = buffReader.readLine()).startsWith("Query: "))
+ {
+ len += nextLine.length()+1;
+ sbuff.append(nextLine+"\n");
+ }
+
+ if(nextLine != null)
+ {
+ len += nextLine.length()+1;
+ sbuff.append(nextLine+"\n");
+ if(nextLine.startsWith("Query:"))
+ {
+ ind1 = nextLine.indexOf(" ",8);
+ int start = Integer.parseInt(nextLine.substring(7,ind1).trim());
+ hit.setQueryStart(start);
+ hit.setQueryEnd(Integer.parseInt(nextLine.substring(nextLine.lastIndexOf(" ")).trim()));
+ }
+ }
+
+// buffReader.reset();
}
else if( (ind1 = line.indexOf("Identities = ")) > -1)
{
@@ -226,6 +263,29 @@ public class FastaTextPane extends JScrollPane
}
else if( (ind1 = line.indexOf(" Length = ")) > -1)
hit.setLength(line.substring(ind1+11));
+ else if(line.startsWith("Query: "))
+ hit.setQueryEnd(Integer.parseInt(line.substring(line.lastIndexOf(" ")).trim()));
+ else if(line.startsWith("Query="))
+ {
+ int ind2 = 0;
+ ind1 = line.indexOf(" letters)");
+ if(ind1 == -1)
+ {
+ String nextLine = null;
+ while((nextLine = buffReader.readLine()).indexOf(" letters)") < -1)
+ {
+ len += nextLine.length()+1;
+ sbuff.append(nextLine+"\n");
+ }
+ line = nextLine;
+ ind1 = nextLine.indexOf(" letters)");
+ ind2 = nextLine.indexOf("(");
+ }
+ else
+ ind2 = line.indexOf("(");
+
+ qlen = line.substring(ind2+1,ind1).trim();
+ }
textPosition += len;
}
diff --git a/uk/ac/sanger/artemis/editor/HitInfo.java b/uk/ac/sanger/artemis/editor/HitInfo.java
index f1c3959e1..c8f84a56c 100644
--- a/uk/ac/sanger/artemis/editor/HitInfo.java
+++ b/uk/ac/sanger/artemis/editor/HitInfo.java
@@ -49,6 +49,9 @@ public class HitInfo
private String desc = null;
/** Sequence length */
private String length = null;
+ /** Query length */
+ private int queryLength = 0;
+
/** */
private String opt = null;
private String zscore = null;
@@ -71,10 +74,13 @@ public class HitInfo
private int startPosition = 0;
/** end position of this hit in the results output */
private int endPosition = 0;
-
/** collection of GO terms */
private Vector go;
-
+ /** query hit start point */
+ private int startQuery;
+ /** query hit end point */
+ private int endQuery;
+
public HitInfo(String header, String format)
{
header = header.trim();
@@ -168,6 +174,53 @@ public class HitInfo
}
+
+ /**
+ *
+ * Get the start position for the query sequence in the alignment.
+ * @return startQuery
+ *
+ */
+ protected int getQueryStart()
+ {
+ return startQuery;
+ }
+
+ /**
+ *
+ * Get the end position for the query sequence in the alignment.
+ * @return endQuery
+ *
+ */
+ protected int getQueryEnd()
+ {
+ return endQuery;
+ }
+
+
+ /**
+ *
+ * Set the start position for the query sequence in the alignment.
+ * @param startQuery startQuery
+ *
+ */
+ protected void setQueryStart(int startQuery)
+ {
+ this.startQuery = startQuery;
+ }
+
+ /**
+ *
+ * Set the end position for the query sequence in the alignment.
+ * @param endQuery endQuery
+ *
+ */
+ protected void setQueryEnd(int endQuery)
+ {
+ this.endQuery = endQuery;
+ }
+
+
/**
*
* Set the start position of the alignment in the
@@ -192,6 +245,29 @@ public class HitInfo
this.endPosition = endPosition;
}
+ /**
+ *
+ * Set the query sequence length.
+ * @param queryLength query sequence length.
+ *
+ */
+ protected void setQueryLength(int queryLength)
+ {
+ this.queryLength = queryLength;
+ }
+
+ /**
+ *
+ * Get the query sequence length.
+ * @return query sequence length.
+ *
+ */
+ protected int getQueryLength()
+ {
+ return queryLength;
+ }
+
+
/**
*
* Set the sequence length.
--
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