Changeset 4439

Timestamp:

Mar 11, 2013, 12:23:25 PM (10 years ago)

Author:

olle

Message:

Refs #799. Proteios SE spectrum viewer updated to indicate the zoom region with a gray rectangle in the original spectrum, in case both a zoomed and original spectrum are shown:

1. Class/file action/peakList/PeakAnnotationUtil.java in client/servlet/ is updated with a new public method void markZoomMassRange(BufferedImage image, Double massCutoffMin, Double massCutoffMax), that marks a mass region by drawing a rectangle in an existing mass spectrum image. It obtains values of the lowest and highest masses in the spectrum, as well as the spectrum area left and right offsets in pixels from values of instance variables, so these must have been set before the method is called. Existing public method void annotateMassValues(BufferedImage image, SpectrumInterface spectrum) is updated to set these values, since it is normally called before the new method.
2. Classes/files action/peakList/PlotFileSpectrum.java and action/peakList/PlotSpectrum.java, both in client/servlet/, are updated in protected method void runMe() to obtain value of new valid parameter VBoolean VMASSCUTOFFMARKUPONLY and if its value is true, ignore the cutoff values when obtaining the spectra (i.e. this spectra is not zoomed), and call method void markZoomMassRange(BufferedImage image, Double massCutoffMin, Double massCutoffMax) in the PeakAnnotationUtil object used to annotate the spectrum.
3. Classes/files action/file/InspectActiveSpectrumFile.java, action/hit/ViewActiveHitSpectrum.java, action/peakList/ViewActivePeakList.java, and action/spectrumSearch/ViewActivePeptideSearchResult.java, all in client/servlet/, are updated to add mass cutoff values to valid parameters VMASSCUTOFFLOWSTR and VMASSCUTOFFHIGHSTR, and set value of valid parameter VMASSCUTOFFMARKUPONLY to true for the view action used for the original spectrum plot.

Location:

trunk/client/servlet/src/org/proteios/action

Files:

• file/InspectActiveSpectrumFile.java (modified) (1 diff)
• hit/ViewActiveHitSpectrum.java (modified) (1 diff)
• peakList/PeakAnnotationUtil.java (modified) (2 diffs)
• peakList/PlotFileSpectrum.java (modified) (6 diffs)
• peakList/PlotSpectrum.java (modified) (6 diffs)
• peakList/ViewActivePeakList.java (modified) (1 diff)
• spectrumSearch/ViewActivePeptideSearchResult.java (modified) (1 diff)

trunk/client/servlet/src/org/proteios/action/file/InspectActiveSpectrumFile.java

@@ -412 +412 @@
             viewOriginalAction.addParameter(PlotFileSpectrum.VSPECTRUMID,
             spectrumId);
+            viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFLOWSTR,
+                massCutoffLowStr);
+            viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFHIGHSTR,
+                massCutoffHighStr);
+            viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFMARKUPONLY,
+                true);
             plotOriginal.setViewAction(viewOriginalAction);
             plotOriginal.setHeight(PlotFileSpectrum.HEIGHT);

trunk/client/servlet/src/org/proteios/action/hit/ViewActiveHitSpectrum.java

@@ -246 +246 @@
         viewOriginalAction.addParameter(FormFactory.VID, hitPeakListFileId);
         viewOriginalAction.addParameter(PlotFileSpectrum.VSPECTRUMID, spectrumId);
+        viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFLOWSTR,
+            massCutoffLowStr);
+        viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFHIGHSTR,
+            massCutoffHighStr);
+        viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFMARKUPONLY,
+            true);
         plotOriginal.setViewAction(viewOriginalAction);
         plotOriginal.setHeight(PlotFileSpectrum.HEIGHT);

trunk/client/servlet/src/org/proteios/action/peakList/PeakAnnotationUtil.java

@@ -33 +33 @@
 
 import static java.awt.Color.BLUE;
+import static java.awt.Color.GRAY;
 import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
@@ -316 +317 @@
       graphics.drawString(massStr, xCoord, (height - yCoord));
     }
+    // Set spectrum offset left and right pixel values
+    setSpectrumOffsetLeft(xSpectrumOffsetLeft);
+    setSpectrumOffsetRight(xSpectrumOffsetRight);
+        // Set spectrum limit mass min and max values
+        setSpectrumLimitMassMin(massMin);
+        setSpectrumLimitMassMax(massMax);
+  }
+
+
+  /**
+   * Marks a mass region by drawing a rectangle
+   * in an existing mass spectrum image.
+   * 
+   * @param image BufferedImage Input mass spectrum image to mark mass region in.
+   * @param massCutoffMin Double The low mass cutoff value for the markup region.
+   * @param massCutoffMax Double The high mass cutoff value for the markup region.
+   */
+  public void markZoomMassRange(BufferedImage image, Double massCutoffMin, Double massCutoffMax)
+  {
+    // If no mass spectrum image, return directly
+    if (image == null)
+    {
+      return;
+    }
+    // Get spectrum offset left and right pixel values
+    int xSpectrumOffsetLeft = getSpectrumOffsetLeft();
+    int xSpectrumOffsetRight = getSpectrumOffsetRight();
+        // Get spectrum limit mass min and max values
+        Double massMin = getSpectrumLimitMassMin();
+        Double massMax = getSpectrumLimitMassMax();
+    // If any other input value is missing, return directly
+    if (massCutoffMin == null || massCutoffMax == null || massMin == null || massMax == null || xSpectrumOffsetLeft < 0 || xSpectrumOffsetRight < 0)
+    {
+      return;
+    }
+    //
+    double massRange = 1.0;
+    if (massMin < massMax)
+    {
+      massRange = massMax - massMin;
+    }
+    log.debug("massMin = " + massMin + " massMax = " + massMax + " massRange = " + massRange);
+    /*
+     * The positioning of mass value markers above (or near)
+     * the top of a mass spectrum peak is determined by
+     * a type of dead reckoning, as use of the JFreeChart
+     * package to draw the mass spectra itself does not
+     * give any feedback for the position of the top of
+     * a mass peak, which depends on the offsets of the
+     * spectrum drawing area in the image, when space for
+     * scales and labels have been allocated. The available
+     * input are the width and height of the image, plus
+     * the mass and intensity values of the spectra.
+     * Based on the graphical output for typical standard
+     * choices of spectra, the needed offsets have been
+     * determined by trial and error to a degree that
+     * hopefully is sufficient for an adequate placement
+     * of the markers.
+     */
+    /*
+     * The following offsets are based on the following input:
+     * width = 400
+     * height = 300
+     * min mass = 110
+     * max mass = 1022
+     * max intensity = 3361
+     */
+    // Use coordinate system with origin at lower left corner
+    int width = image.getWidth();
+    int height = image.getHeight();
+    // Offsets in pixels for inner drawing area without scales and labels
+    //int xInnerAreaOffsetLeft = 58;
+    //int xInnerAreaOffsetRight = 12;
+    int yInnerAreaOffsetBottom = 36;
+    int yInnerAreaOffsetTop = 30;
+    // Offsets in pixels for mass spectrum area relative to inner drawing area
+    //int xInnerAreaFirstPeakOffset = 18;
+    //int xInnerAreaLastPeakOffset = 13;
+    int yInnerAreaPeakBottomOffset = 0;
+    int yInnerAreaPeakTopOffset = 10;
+    // Offsets in pixels for mass spectrum area relative to full drawing area
+    int ySpectrumOffsetBottom = yInnerAreaOffsetBottom + yInnerAreaPeakBottomOffset;
+    int ySpectrumOffsetTop = yInnerAreaOffsetTop + yInnerAreaPeakTopOffset;
+    int spectrumAreaWidth = width - xSpectrumOffsetLeft - xSpectrumOffsetRight;
+    int spectrumAreaHeight = height - ySpectrumOffsetBottom - ySpectrumOffsetTop;
+    log.debug("width = " + width + " height = " + height);
+    log.debug("spectrumAreaWidth = " + spectrumAreaWidth + " spectrumAreaHeight = " + spectrumAreaHeight);
+    int xCutoffMinCoord = xSpectrumOffsetLeft + (int) (spectrumAreaWidth*((massCutoffMin - massMin)/massRange));
+    int xCutoffMaxCoord = xSpectrumOffsetLeft + (int) (spectrumAreaWidth*((massCutoffMax - massMin)/massRange));
+    // Prepare to add mass value annotations to mass spectrum image
+    Graphics2D graphics = image.createGraphics();
+    // Copy original buffer
+    graphics.drawImage(image, 0, 0, null, null);
+    graphics.setColor(GRAY);
+    // Draw rectangle containing zoom region
+    int zoomRectWidth = xCutoffMaxCoord - xCutoffMinCoord;
+    int zoomRectHeight = height - yInnerAreaOffsetBottom - yInnerAreaOffsetTop - 2;
+    graphics.drawRect(xCutoffMinCoord, yInnerAreaOffsetTop - 3, zoomRectWidth, zoomRectHeight);
   }
 

trunk/client/servlet/src/org/proteios/action/peakList/PlotFileSpectrum.java

@@ -50 +50 @@
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
+import se.lu.thep.waf.constraints.VBoolean;
 import se.lu.thep.waf.constraints.VFloat;
 import se.lu.thep.waf.constraints.VString;
@@ -67 +68 @@
   public static final VString VMASSCUTOFFLOWSTR = MassRangeForm.VMASSCUTOFFLOWSTR;
   public static final VString VMASSCUTOFFHIGHSTR = MassRangeForm.VMASSCUTOFFHIGHSTR;
+  public static final VBoolean VMASSCUTOFFMARKUPONLY = new VBoolean("massCutoffMarkupOnly", false);
   private int spectrumOffsetLeft = -1;
   private int spectrumOffsetRight = -1;
@@ -199 +201 @@
           massCutoffHigh = massCutoffLowTmp;
         }
+        // Get flag to only use mass cutoff values for markup
+        Boolean massCutoffMarkupOnly = getValidBoolean(VMASSCUTOFFMARKUPONLY);
+        if (massCutoffMarkupOnly == null)
+        {
+          massCutoffMarkupOnly = false;
+        }
         log.debug("fileId = " + peakListFileId);
         log.debug("spectrumId = \"" + spectrumId + "\"");
@@ -205 +213 @@
         log.debug("massCutoffLow = " + massCutoffLow);
         log.debug("massCutoffHigh = " + massCutoffHigh);
+        log.debug("massCutoffMarkupOnly = " + massCutoffMarkupOnly);
         /***********************************************************************
             * Get peakListFile data
@@ -271 +280 @@
             log.debug("useTitle = " + useTitle + " spectrumId = \"" + spectrumId + "\"");
             spectrum = peakListFileReader.getSpectrum(spectrumId);
-            // Restrict spectrum to specified mass range, if defined
-            spectrum = zoomSpectrum(spectrum, massCutoffLow, massCutoffHigh);
+            if (!massCutoffMarkupOnly)
+            {
+                // Restrict spectrum to specified mass range, if defined
+                spectrum = zoomSpectrum(spectrum, massCutoffLow, massCutoffHigh);
+            }
             if (spectrum != null)
             {
@@ -333 +345 @@
         PeakAnnotationUtil peakAnnotationUtil = new PeakAnnotationUtil();
         peakAnnotationUtil.annotateMassValues(image, spectrum);
+        // Mark zoom region if requested
+        if (massCutoffMarkupOnly)
+        {
+          Double massCutoffLowDbl = null;
+          Double massCutoffHighDbl = null;
+          if (massCutoffLow != null)
+          {
+            massCutoffLowDbl = Double.valueOf((double)massCutoffLow);
+          }
+          if (massCutoffHigh != null)
+          {
+            massCutoffHighDbl = Double.valueOf((double)massCutoffHigh);
+          }
+          peakAnnotationUtil.markZoomMassRange(image, massCutoffLowDbl, massCutoffHighDbl);
+        }
         /***********************************************************************
             * Send plot

trunk/client/servlet/src/org/proteios/action/peakList/PlotSpectrum.java

@@ -45 +45 @@
 import se.lu.thep.waf.ActionException;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
+import se.lu.thep.waf.constraints.VBoolean;
 import se.lu.thep.waf.constraints.VString;
 import java.awt.image.BufferedImage;
@@ -65 +66 @@
   public static final VString VMASSCUTOFFLOWSTR = new VString("massCutoffLowStr", 0, 255, false);
   public static final VString VMASSCUTOFFHIGHSTR = new VString("massCutoffHighStr", 0, 255, false);
+  public static final VBoolean VMASSCUTOFFMARKUPONLY = new VBoolean("massCutoffMarkupOnly", false);
   private int spectrumOffsetLeft = -1;
   private int spectrumOffsetRight = -1;
@@ -183 +185 @@
       massCutoffHigh = massCutoffLowTmp;
     }
+        // Get flag to only use mass cutoff values for markup
+        Boolean massCutoffMarkupOnly = getValidBoolean(VMASSCUTOFFMARKUPONLY);
+        if (massCutoffMarkupOnly == null)
+        {
+          massCutoffMarkupOnly = false;
+        }
     log.debug("peakListId = " + peakListId);
     log.debug("massCutoffLowStr = \"" + massCutoffLowStr + "\"");
@@ -188 +196 @@
     log.debug("massCutoffLow = " + massCutoffLow);
     log.debug("massCutoffHigh = " + massCutoffHigh);
+        log.debug("massCutoffMarkupOnly = " + massCutoffMarkupOnly);
     DbControl dc = newDbControl();
     PeakList pl = PeakList.getById(dc, peakListId);
@@ -228 +237 @@
     }
     SpectrumInterface spectrum = null;
-    // Restrict spectrum to specified mass range, if defined
-    spectrum = zoomSpectrum(spectrumOrig, massCutoffLow, massCutoffHigh);
+        if (!massCutoffMarkupOnly)
+        {
+            // Restrict spectrum to specified mass range, if defined
+            spectrum = zoomSpectrum(spectrum, massCutoffLow, massCutoffHigh);
+        }
     if (spectrum != null)
     {
@@ -295 +307 @@
     PeakAnnotationUtil peakAnnotationUtil = new PeakAnnotationUtil();
     peakAnnotationUtil.annotateMassValues(image, spectrum);
+        // Mark zoom region if requested
+        if (massCutoffMarkupOnly)
+        {
+          Double massCutoffLowDbl = null;
+          Double massCutoffHighDbl = null;
+          if (massCutoffLow != null)
+          {
+            massCutoffLowDbl = Double.valueOf((double)massCutoffLow);
+          }
+          if (massCutoffHigh != null)
+          {
+            massCutoffHighDbl = Double.valueOf((double)massCutoffHigh);
+          }
+          peakAnnotationUtil.markZoomMassRange(image, massCutoffLowDbl, massCutoffHighDbl);
+        }
     /***********************************************************************
      * Send plot

trunk/client/servlet/src/org/proteios/action/peakList/ViewActivePeakList.java

@@ -131 +131 @@
             PlotSpectrum.class, "ViewOriginal");
             viewOriginalAction.addParameter(FormFactory.VID, peakListId);
+            viewOriginalAction.addParameter(PlotSpectrum.VMASSCUTOFFLOWSTR,
+                massCutoffLowStr);
+            viewOriginalAction.addParameter(PlotSpectrum.VMASSCUTOFFHIGHSTR,
+                massCutoffHighStr);
+            viewOriginalAction.addParameter(PlotSpectrum.VMASSCUTOFFMARKUPONLY,
+                true);
             plotOriginal.setViewAction(viewOriginalAction);
             plotOriginal.setHeight(PlotSpectrum.HEIGHT);

trunk/client/servlet/src/org/proteios/action/spectrumSearch/ViewActivePeptideSearchResult.java

@@ -198 +198 @@
                 viewOriginalAction.addParameter(FormFactory.VID, peakListFile.getId());
                 viewOriginalAction.addParameter(MassRangeForm.VSPECTRUMID, spectrumId);
+                viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFLOWSTR,
+                    massCutoffLowStr);
+                viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFHIGHSTR,
+                    massCutoffHighStr);
+                viewOriginalAction.addParameter(PlotFileSpectrum.VMASSCUTOFFMARKUPONLY,
+                    true);
                 plotOriginal.setViewAction(viewOriginalAction);
                 plotOriginal.setHeight(PlotFileSpectrum.HEIGHT);