- split chart by allele

- read info on current position

build.xml

@@ -249,4 +249,13 @@
         </antcall>
     </target>
 
+    <!-- Deploy the application -->
+    <target name="deploy">
+        <copy todir="${deploy.dir}" overwrite="true">
+            <fileset dir="${dist.dir}">
+                <include name="lib/**"/>
+            </fileset>
+            <fileset file="${dist.dir}${jar.name}"/>
+        </copy>
+    </target>
 </project>

launcher/build.xml

@@ -89,7 +89,7 @@
 
 
     <!-- Sign all jars if a keystore is defined -->
-    <target name="sign-jars" if="keystore">
+    <target name="sign-jars" >
         <signjar jar="${jar.path}" alias="${alias}" keypass="${key-password}" storepass="${store-password}"
                  keystore="${keystore}"/>
     </target>

nbproject/project.properties

@@ -155,7 +155,7 @@ run.classpath=\
 # Space-separated list of JVM arguments used when running the project
 # (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value
 # or test-sys-prop.name=value to set system properties for unit tests):
-run.jvmargs=
+run.jvmargs=-Xmx900M -Xms512M
 run.test.classpath=\
     ${javac.test.classpath}:\
     ${build.test.classes.dir}

src/com/iontorrent/data/FlowDistribution.java

@@ -4,6 +4,7 @@
  */
 package com.iontorrent.data;
 
+import java.util.ArrayList;
 import java.util.TreeMap;
 
 /**
@@ -18,6 +19,7 @@ public class FlowDistribution {
     private int nrflows;
     /** the chromosome location */
     private int location;
+    ArrayList<ReadInfo> readinfos;
 
     public FlowDistribution(int location, int nrflows, TreeMap<Short, Integer> map, String name, String information) {
         this.map = map;
@@ -39,7 +41,7 @@ public String toCsv(int binsize) {
         String nl = "\n";
         StringBuilder csv = new StringBuilder();
         csv = csv.append(getInformation());
-        csv = csv.append("flow value, count\n");
+        csv = csv.append(nl).append("flow value, count\n");
         for (int b = 0; b < bins.length; b++) {
             csv = csv.append(b * binsize).append(",").append(bins[b]).append(nl);
         }
@@ -56,7 +58,17 @@ public String toJson() {
         buf.append("}\n");
         return buf.toString();
     }
-
+    public String getReadInfoString() {
+       String nl = "\n";
+        StringBuilder csv = new StringBuilder();
+        csv = csv.append(getInformation());
+        csv = csv.append(nl).append(ReadInfo.getHeader()).append(nl);
+        for (ReadInfo ri: readinfos) {
+            csv = csv.append(ri.toCsv()).append(nl);
+        }
+        csv = csv.append(nl);
+        return csv.toString(); 
+    }
     public int[] getBinnedData(int binsize) {
         int maxx = 0;
         for (Short x : map.keySet()) {
@@ -118,4 +130,8 @@ public int getMaxX() {
         }
         return maxx;
     }
+
+    public void setReadInfos(ArrayList<ReadInfo> readinfos) {
+       this.readinfos = readinfos;
+    }
 }

src/com/iontorrent/data/ReadInfo.java

@@ -0,0 +1,43 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package com.iontorrent.data;
+
+/**
+ *
+ * @author Chantal Roth
+ */
+public class ReadInfo {
+    String readname;
+    int flowposition;
+    int flowvalue;
+    char base;
+
+    public ReadInfo(String readname, int flowposition,int flowvalue, char base) {
+        this.readname = readname;
+        this.flowposition = flowposition;
+        this.flowvalue = flowvalue;
+        this.base = base;
+    }
+    public int getFlowPosition() {
+        return flowposition;
+    }
+    public char getBase() {
+        return base;
+    }
+    public String getReadName() {
+        return readname;
+    }
+    public static String getHeader() {
+       return "Read name, flow position, base, flow value";
+    }
+    public String toCsv() {
+        StringBuilder b = new StringBuilder();
+        b = b.append(readname).append(",").append(flowposition).append(",").append(base).append(",").append(flowvalue);
+        return b.toString();
+    }
+    public String toString() {
+        return toCsv();
+    }
+}

src/com/iontorrent/views/FlowSignalDistributionPanel.form

@@ -56,6 +56,20 @@
             <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="btnCopyJsonActionPerformed"/>
           </Events>
         </Component>
+        <Component class="javax.swing.JButton" name="jButton1">
+          <Properties>
+            <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.editors2.IconEditor">
+              <Image iconType="3" name="/com/iontorrent/views/copyr.png"/>
+            </Property>
+            <Property name="toolTipText" type="java.lang.String" value="show read info"/>
+            <Property name="focusable" type="boolean" value="false"/>
+            <Property name="horizontalTextPosition" type="int" value="0"/>
+            <Property name="verticalTextPosition" type="int" value="3"/>
+          </Properties>
+          <Events>
+            <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButton1ActionPerformed"/>
+          </Events>
+        </Component>
         <Component class="javax.swing.JButton" name="btnSave">
           <Properties>
             <Property name="icon" type="javax.swing.Icon" editor="org.netbeans.modules.form.editors2.IconEditor">

src/com/iontorrent/views/FlowSignalDistributionPanel.java

@@ -113,7 +113,7 @@ private CategoryDataset createCategoryDataset() {
         }
         return dataset;
     }
-   
+
     private XYSeriesCollection createXYDataset() {
         XYSeriesCollection dataset = new XYSeriesCollection();
         for (int i = 0; i < distributions.length; i++) {
@@ -132,14 +132,14 @@ private JComponent createChart() {
         String yaxis = "count";
 
         XYItemRenderer renderer;
-        
+
         NumberAxis xax = new NumberAxis(xaxis);
         NumberAxis yax = new NumberAxis(yaxis);
         JFreeChart freechart = null;
         // could be another chart option
         // XYSplineRenderer renderer = new XYSplineRenderer();
-        
-        if (chart_type == ChartConfigPanel.TYPE_BAR) {            
+
+        if (chart_type == ChartConfigPanel.TYPE_BAR) {
             CategoryDataset dataset = createCategoryDataset();
             freechart = ChartFactory.createBarChart(
                     plotTitle, // chart title
@@ -151,15 +151,15 @@ private JComponent createChart() {
                     true, // tooltips?
                     false // URLs?
                     );
-             freechart.getCategoryPlot().setForegroundAlpha(0.75f);
-          
+            freechart.getCategoryPlot().setForegroundAlpha(0.75f);
+
         } else if (chart_type == ChartConfigPanel.TYPE_LINE) {
             renderer = new XYLineAndShapeRenderer();
             XYSeriesCollection dataset = createXYDataset();
             XYPlot plot = new XYPlot(dataset, xax, yax, renderer);
             freechart = new JFreeChart(plot);
             plot.setForegroundAlpha(0.75f);
-           
+
         } else if (chart_type == ChartConfigPanel.TYPE_AREA) {
             renderer = new XYAreaRenderer(XYAreaRenderer.AREA);
             XYSeriesCollection dataset = createXYDataset();
@@ -175,7 +175,7 @@ private JComponent createChart() {
         } else {
             freechart.addSubtitle(new TextTitle(information + ", " + bininfo));
         }
-       
+
         ChartPanel chartPanel = new ChartPanel(freechart);
         chartPanel.setPreferredSize(new java.awt.Dimension(500, 270));
         return chartPanel;
@@ -184,7 +184,7 @@ private JComponent createChart() {
     private XYSeries createDataset(FlowDistribution dist) {
         int[] bins = dist.getBinnedData(binsize);
 
-        p("Flow Dist name: "+dist.getName());
+        p("Flow Dist name: " + dist.getName());
         XYSeries xy = new XYSeries(dist.getName());
         for (int b = 0; b < bins.length; b++) {
             xy.add(b * binsize, bins[b]);
@@ -205,11 +205,19 @@ private String getJsonString() {
         StringBuilder json = new StringBuilder();
         //json = json.append(information).append("\n\n");
         for (int i = 0; i < distributions.length; i++) {
-            json = json.append(distributions[i].toJson());
+            json = json.append("\n").append(distributions[i].toJson());
         }
         return json.toString();
     }
 
+    private String getReadString() {
+        StringBuilder rinfo = new StringBuilder();
+        for (int i = 0; i < distributions.length; i++) {
+            rinfo = rinfo.append("\n").append(distributions[i].getReadInfoString());
+        }
+        return rinfo.toString();
+    }
+
     private void p(String msg) {
         log.info(msg);
     }
@@ -230,6 +238,7 @@ private void initComponents() {
         buttonToolBar = new javax.swing.JToolBar();
         btnCopy = new javax.swing.JButton();
         btnCopyJson = new javax.swing.JButton();
+        jButton1 = new javax.swing.JButton();
         btnSave = new javax.swing.JButton();
         btnConfigure = new javax.swing.JButton();
         btnLeft = new javax.swing.JButton();
@@ -263,6 +272,18 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         });
         buttonToolBar.add(btnCopyJson);
 
+        jButton1.setIcon(new javax.swing.ImageIcon(getClass().getResource("/com/iontorrent/views/copyr.png"))); // NOI18N
+        jButton1.setToolTipText("show read info");
+        jButton1.setFocusable(false);
+        jButton1.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
+        jButton1.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
+        jButton1.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                jButton1ActionPerformed(evt);
+            }
+        });
+        buttonToolBar.add(jButton1);
+
         btnSave.setIcon(new javax.swing.ImageIcon(getClass().getResource("/com/iontorrent/views/save.png"))); // NOI18N
         btnSave.setToolTipText("Save data in .csv file (to be used in Excel for instance)");
         btnSave.setFocusable(false);
@@ -383,6 +404,19 @@ private void btnRightActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRS
             getListener().locationChanged(location + 1);
         }
     }//GEN-LAST:event_btnRightActionPerformed
+
+    private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton1ActionPerformed
+        String readinfo = getReadString();
+        // copy to clipboard
+        StringSelection stringSelection = new StringSelection(readinfo);
+        Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+        clipboard.setContents(stringSelection, null);
+
+        // also show as popup for copy paste
+        JTextArea area = new JTextArea(15, 30);
+        area.setText(readinfo);
+        JOptionPane.showMessageDialog(this, new JScrollPane(area), "Read info string (it is already in the clipboard)", JOptionPane.INFORMATION_MESSAGE);
+    }//GEN-LAST:event_jButton1ActionPerformed
     // Variables declaration - do not modify//GEN-BEGIN:variables
     private javax.swing.JButton btnConfigure;
     private javax.swing.JButton btnCopy;
@@ -391,6 +425,7 @@ private void btnRightActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRS
     private javax.swing.JButton btnRight;
     private javax.swing.JButton btnSave;
     private javax.swing.JToolBar buttonToolBar;
+    private javax.swing.JButton jButton1;
     // End of variables declaration//GEN-END:variables
 
     public void setDistributions(FlowDistribution[] newdist) {

src/org/broad/igv/sam/AbstractAlignment.java

@@ -129,28 +129,38 @@ private void bufAppendFlowSignals(AlignmentBlock block, StringBuffer buf, int of
             FlowSignalSubContext f = block.getFlowSignalSubContext(offset);
             if (null != f && null != f.signals && null != f.bases) {
                 buf.append("FZ = ");
+                StringBuffer spos = new StringBuffer();
+                spos.append("Flow positions = ");
                 for (i=0;i<f.signals.length;i++) {
                     if (null != f.signals[i] && 0 < f.signals[i].length) {
                         if (1 == i) {
                             if (0 < n) {
                                 buf.append(",");
+                                spos.append(",");
                             }
                             buf.append("[");
+                            spos.append("[");
                         }
                         for (j=0;j<f.signals[i].length;j++) {
                             if (1 != i && 0 < n) {
                                 buf.append(",");
+                                 spos.append(",");
                             }
                             buf.append(f.bases[i][j]);
                             buf.append(f.signals[i][j]);
+                            spos.append(f.flownumbers[i][j]);
                             n++;
                         }
                         if (1 == i) {
                             buf.append("]");
+                            spos.append("]");
                         }
                     }
                 }
+                buf.append("<br>").append(spos);
                 buf.append("<br>");
+                // maybe also add flow order?
+
             }
         }
     }

src/org/broad/igv/sam/AlignmentBlockFS.java

@@ -20,7 +20,7 @@ protected AlignmentBlockFS(int start, byte[] bases, byte[] qualities, FlowSignal
     }
 
     public FlowSignalSubContext getFlowSignalSubContext(int offset) {
-        return new FlowSignalSubContext(this.fContext.signals[offset], this.fContext.bases[offset]);
+        return new FlowSignalSubContext(this.fContext.signals[offset], this.fContext.bases[offset], this.fContext.flownumbers[offset]);
     }