diff --git a/uk/ac/sanger/artemis/components/alignment/JamView.java b/uk/ac/sanger/artemis/components/alignment/JamView.java
index b196ba9a543d4f3ed34b6fda896dd143a0c6046f..db4ed9d497ba4d57f7581c865805e1ef34275ee5 100644
--- a/uk/ac/sanger/artemis/components/alignment/JamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/JamView.java
@@ -1,4 +1,26 @@
-
+/* JamView
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2009 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
package uk.ac.sanger.artemis.components.alignment;
import java.awt.BasicStroke;
@@ -61,7 +83,7 @@ public class JamView extends JPanel
private Hashtable<String, Integer> seqLengths = new Hashtable<String, Integer>();
private Vector<String> seqNames = new Vector<String>();
private String bam;
- private String sam;
+
private EntryGroup entryGroup;
private JScrollPane jspView;
private JComboBox combo;
@@ -121,10 +143,13 @@ public class JamView extends JPanel
*/
private void readHeader()
{
- String cmd[] = { "/Users/tjc/BAM/samtools-0.1.5c/samtools",
+ String samtoolCmd = "";
+ if(System.getProperty("samtoolDir") != null)
+ samtoolCmd = System.getProperty("samtoolDir");
+ String cmd[] = { samtoolCmd+File.separator+"samtools",
"view", "-H", bam };
- RunSamTools samtools = new RunSamTools(cmd, null, null);
+ RunSamTools samtools = new RunSamTools(cmd, null, null, null);
if(samtools.getProcessStderr() != null)
System.out.println(samtools.getProcessStderr());
@@ -181,42 +206,17 @@ public class JamView extends JPanel
for(int i=0; i<cmd.length;i++)
System.out.print(cmd[i]+" ");
System.out.println();
- RunSamTools samtools = new RunSamTools(cmd, null, null);
+
+ if(readsInView == null)
+ readsInView = new Vector<Read>();
+ else
+ readsInView.clear();
+ RunSamTools samtools = new RunSamTools(cmd, null, null, readsInView);
if(samtools.getProcessStderr() != null)
System.out.println(samtools.getProcessStderr());
- sam = samtools.getProcessStdout();
-
- StringReader samReader = new StringReader(sam);
- BufferedReader buff = new BufferedReader(samReader);
- String line;
- try
- {
- if(readsInView == null)
- readsInView = new Vector<Read>();
- else
- readsInView.clear();
- while((line = buff.readLine()) != null)
- {
- String fields[] = line.split("\t");
-
- Read pread = new Read();
- pread.qname = fields[0];
- pread.flag = Integer.parseInt(fields[1]);
- pread.rname = fields[2];
- pread.pos = Integer.parseInt(fields[3]);
- pread.mapq = Short.parseShort(fields[4]);
- pread.mpos = Integer.parseInt(fields[7]);
- pread.isize = Integer.parseInt(fields[8]);
- pread.seq = fields[9];
- readsInView.add(pread);
- }
- }
- catch (IOException e)
- {
- e.printStackTrace();
- }
+ samtools.waitForStdout();
}
/**
@@ -465,6 +465,8 @@ public class JamView extends JPanel
{
public void itemStateChanged(ItemEvent e)
{
+ laststart = -1;
+ lastend = -1;
setZoomLevel(JamView.this.nbasesInView);
}
});
@@ -492,7 +494,6 @@ public class JamView extends JPanel
{
public void mouseClicked(MouseEvent e)
{
- System.out.println("CLICK");
JamView.this.requestFocus();
}
});
@@ -629,20 +630,6 @@ public class JamView extends JPanel
return entry;
}
- class Read
- {
- String qname; // query name
- int flag; // bitwise flag
- String rname; // reference name
- int pos; // leftmost coordinate
- short mapq; // MAPping Quality
- String cigar; // extended CIGAR string
- String mrnm; // Mate Reference sequence NaMe; Ò=Ó if the same as rname
- int mpos; // leftmost Mate POSition
- int isize; // inferred Insert SIZE
- String seq; // query SEQuence; Ò=Ó for a match to the reference; n/N/. for ambiguity
- }
-
class ReadComparator implements Comparator
{
public int compare(Object o1, Object o2)
diff --git a/uk/ac/sanger/artemis/components/alignment/Read.java b/uk/ac/sanger/artemis/components/alignment/Read.java
new file mode 100644
index 0000000000000000000000000000000000000000..02d765664fa92c230f2dd8aba62a11526fde1d8d
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/Read.java
@@ -0,0 +1,38 @@
+/* Read
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2009 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.components.alignment;
+
+class Read
+{
+ String qname; // query name
+ int flag; // bitwise flag
+ String rname; // reference name
+ int pos; // leftmost coordinate
+ short mapq; // MAPping Quality
+ String cigar; // extended CIGAR string
+ String mrnm; // Mate Reference sequence NaMe; Ò=Ó if the same as rname
+ int mpos; // leftmost Mate POSition
+ int isize; // inferred Insert SIZE
+ String seq; // query SEQuence; Ò=Ó for a match to the reference; n/N/. for ambiguity
+}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/RunSamTools.java b/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
index 2ac1284d4116bb25aee4456eaa61a74cd737fdd3..47dda18fc8bd63722aed9db6a9c0e02da1fb7c41 100644
--- a/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
+++ b/uk/ac/sanger/artemis/components/alignment/RunSamTools.java
@@ -1,8 +1,30 @@
-
+/* RunSamTools
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2009 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
package uk.ac.sanger.artemis.components.alignment;
import java.io.*;
-import javax.swing.JTextArea;
+import java.util.List;
/**
* Used to run an samtools process this reads stdout and
@@ -14,10 +36,10 @@ public class RunSamTools
/** running process */
private Process p;
/** standard out */
- private StringBuffer stdout = new StringBuffer();
+ private List<Read> readsInView;
/** standard error */
private StringBuffer stderr = new StringBuffer();
-
+ private StringBuffer stdout = new StringBuffer();
private String initialIOError = null;
/** running directory */
@@ -26,8 +48,6 @@ public class RunSamTools
private String status;
private StdoutHandler stdouth;
private StderrHandler stderrh;
- private JTextArea textArea;
-
/**
* @param cmd command to run
@@ -35,9 +55,12 @@ public class RunSamTools
* @param project running directory
*/
public RunSamTools(String cmd[],
- String[] envp, File project)
+ String[] envp,
+ File project,
+ List<Read> readsInView)
{
//this.project = project;
+ this.readsInView = readsInView;
status = "0";
Runtime run = Runtime.getRuntime();
@@ -116,29 +139,36 @@ public class RunSamTools
*/
private void readProcessStdout()
{
- BufferedInputStream stdoutStream = null;
+ InputStreamReader stdoutStream = null;
BufferedReader stdoutRead = null;
try
{
//String line;
stdoutStream =
- new BufferedInputStream(p.getInputStream());
+ new InputStreamReader(p.getInputStream());
stdoutRead =
- new BufferedReader(new InputStreamReader(stdoutStream));
-
- char c[] = new char[200];
- int nc = 0;
- String chunk;
-
- while((nc = stdoutRead.read(c,0,200)) != -1)
+ new BufferedReader(stdoutStream);
+
+ String line;
+ while((line = stdoutRead.readLine()) != null)
{
- chunk = new String(c,0,nc);
- stdout = stdout.append(chunk);
- if(textArea != null)
+ if(readsInView != null)
{
- textArea.append(chunk);
- textArea.setCaretPosition(textArea.getDocument().getLength());
+ String fields[] = line.split("\t");
+
+ Read pread = new Read();
+ pread.qname = fields[0];
+ pread.flag = Integer.parseInt(fields[1]);
+ pread.rname = fields[2];
+ pread.pos = Integer.parseInt(fields[3]);
+ pread.mapq = Short.parseShort(fields[4]);
+ pread.mpos = Integer.parseInt(fields[7]);
+ pread.isize = Integer.parseInt(fields[8]);
+ pread.seq = fields[9];
+ readsInView.add(pread);
}
+ else
+ stdout.append(line+"\n");
}
}
catch (IOException io)
@@ -172,59 +202,43 @@ public class RunSamTools
}
/**
- * This method can be called after the process has completed
- * to write the stdout to the project directory.
- */
-// private void writeStdout()
-// {
-// if(project != null)
-// {
-// PrintWriter out = null;
-// String fname = "";
-// try
-// {
-// fname = project.getCanonicalPath() +
-// "/application_stdout";
-// File so = new File(fname);
-//
-// if(!so.exists())
-// so.createNewFile();
-//
-// out = new PrintWriter(new FileWriter(fname,true));
-// out.println(stdout);
-// }
-// catch(IOException ioe)
-// {
-// System.err.println("RunEmbossApplication2: Error writing" +
-// fname);
-// }
-// finally
-// {
-// if(out!=null)
-// out.close();
-// }
-// }
-// }
-
- /**
- * @return standard out
- */
- public String getProcessStdout()
- {
- try
+ * @return standard out
+ */
+ public void waitForStdout()
+ {
+ try
+ {
+ // make sure we hang around for stdout
+ while(stdouth.isAlive())
+ Thread.sleep(10);
+ }
+ catch(InterruptedException ie)
+ {
+ ie.printStackTrace();
+ }
+
+ return;
+ }
+
+ /**
+ * @return standard out
+ */
+ public String getProcessStdout()
{
- // make sure we hang around for stdout
- while(stdouth.isAlive())
- Thread.sleep(10);
- }
- catch(InterruptedException ie)
- {
- ie.printStackTrace();
+ try
+ {
+ // make sure we hang around for stdout
+ while(stdouth.isAlive())
+ Thread.sleep(10);
+ }
+ catch(InterruptedException ie)
+ {
+ ie.printStackTrace();
+ }
+
+ return stdout.toString();
}
-
- return stdout.toString();
- }
-
+
/**
* @return stderr
*/