Changeset 4050

Timestamp:

Dec 7, 2007, 1:57:26 PM (15 years ago)

Author:

Martin Svensson

Message:

Fixes #864 Some core plug-ins report negative progress values in large experiments.

Location:

branches/2.5-stable/src

Files:

• clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java (modified) (2 diffs)
• core/net/sf/basedb/core/Affymetrix.java (modified) (1 diff)
• core/net/sf/basedb/core/RawBioAssay.java (modified) (2 diffs)
• core/net/sf/basedb/core/SpotImages.java (modified) (1 diff)
• core/net/sf/basedb/util/BioAssaySetFilterUtil.java (modified) (4 diffs)
• core/net/sf/basedb/util/IntensityCalculatorUtil.java (modified) (2 diffs)
• plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (3 diffs)
• plugins/core/net/sf/basedb/plugins/LowessNormalization.java (modified) (2 diffs)
• plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) (2 diffs)

branches/2.5-stable/src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java

@@ -468 +468 @@
     template.writeHeaders();
     
-    int numExported = 0;
+    long numExported = 0;
     ResultIterator result = null;
     try
@@ -506 +506 @@
           if (progress != null)
           {
-            int percent = (int)(100f * numExported / totalItems);
+            int percent = (int)(100L * numExported / totalItems);
             progress.display(percent, numExported + " of " + totalItems + " done.");
           }

branches/2.5-stable/src/core/net/sf/basedb/core/Affymetrix.java

@@ -357 +357 @@
       if (hasProgress && (index % progressInterval == 0))
       {
-        int percent = 5 + 90 * index / numProbesets;
+        int percent = 5 + (int)(90L * (long)index / numProbesets);
         int remain = numProbesets - index;
         String created = create ? "; " + numCreated + " created" : "";

branches/2.5-stable/src/core/net/sf/basedb/core/RawBioAssay.java

@@ -1122 +1122 @@
       DataQuery<RawData> rawQuery = getRawData();
       DataResultIterator<RawData> result = rawQuery.iterate(dc);
-      int numValidated = 0;
+      long numValidated = 0;
       int numTotal = getNumDbSpots();
       while (result.hasNext())
@@ -1183 +1183 @@
         if (progress != null && numValidated % 100 == 0)
         {
-          int percent = 10 + (90 * numValidated) / numTotal;
+          int percent = 10 + ((int)(90L * numValidated) / numTotal);
           progress.display(percent, "Validated " + numValidated + " of " + numTotal + " spots.");
         }

branches/2.5-stable/src/core/net/sf/basedb/core/SpotImages.java

@@ -472 +472 @@
           if (progress != null) 
           {
-            int spotsDone = spotImagesPerImage*imageNumber;
-            int percent = 10 + 90 * spotsDone / totalSpots;
+            long spotsDone = spotImagesPerImage*imageNumber;
+            int percent = 10 + (int)(90L * spotsDone / totalSpots);
             progress.display(percent, "Generating spot images ("+spotsDone+" done)...");
           }

branches/2.5-stable/src/core/net/sf/basedb/util/BioAssaySetFilterUtil.java

@@ -123 +123 @@
     }
     
-    int spotsDone = 0;
+    long spotsDone = 0;
     int spotsAfter = 0;
     if (progress != null) progress.display(10, "Filtering spots (0 done; "+spotsTotal+" total)...");
@@ -139 +139 @@
       if (progress != null) 
       {
-        int percent = 10 + 90 * spotsDone / spotsTotal;
+        int percent = 10 + (int)(90L * spotsDone / spotsTotal);
         progress.display(percent, 
           "Filtering spot intensities ("+spotsDone+" done; "+spotsTotal+" total)...");
@@ -205 +205 @@
     // Prepare progress reporting
     int interval = 10;  // Update progress after this many spots >= 10
-    int spotsDone = 0;
+    long spotsDone = 0;
     int spotsAfter = 0;
     if (progress != null)
@@ -236 +236 @@
             if (spotsDone % interval == 0)
             {
-              int percent = 10 + 90 * spotsDone / spotsTotal;
+              int percent = 10 + (int)(90L * spotsDone / spotsTotal);
               progress.display(percent, 
                 "Filtering spot intensities ("+spotsDone+" done; "+spotsTotal+" total)...");

branches/2.5-stable/src/core/net/sf/basedb/util/IntensityCalculatorUtil.java

@@ -305 +305 @@
     int maxPosition = 0;
     
-    int spotsDone = 0; // Number of calculated spots
+    long spotsDone = 0; // Number of calculated spots
     int totalSpots = 0; // Total number of spots
     int interval = 0; // Interval between reporter to the progress reporter
@@ -426 +426 @@
           if (spotsDone % interval == 0)
           {
-            int percent = 10 + 90 * spotsDone / totalSpots;
+            int percent = 10 + (int)((90L * spotsDone) / totalSpots);
             progress.display(percent, "Calculating spot intensities ("+spotsDone+" done)...");
           }

branches/2.5-stable/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -685 +685 @@
     int nof_reporters=bioassayset.getNumReporters();
     int progress_report_interval=nof_reporters/10;
-    int nof_processed_reporters=0;
+    long nof_processed_reporters=0;
     while (spotData.hasNext())
     {
       if (progress != null && (nof_processed_reporters%progress_report_interval == 0))
       {
-        progress.display(100 * nof_processed_reporters / nof_reporters,
+        progress.display((int)(100L * nof_processed_reporters / nof_reporters),
                          "Exporting ... " + nof_processed_reporters + " of " +
                          nof_reporters + " done.");
@@ -781 +781 @@
     int nof_spots=bioassayset.getNumSpots();
     int progress_spot_interval=nof_spots/10;
-    int nof_processed_spots=0;
+    long nof_processed_spots=0;
     while (spotData.hasNext())
     {
@@ -791 +791 @@
           (nof_processed_spots%progress_spot_interval == 0))
         {
-          progress.display(100 * nof_processed_spots / nof_spots,
+          progress.display((int)(100L * nof_processed_spots / nof_spots),
                            "Exporting ..." + nof_processed_spots + " of " +
                            nof_spots + " done.");

branches/2.5-stable/src/plugins/core/net/sf/basedb/plugins/LowessNormalization.java

@@ -351 +351 @@
     query.restrict(intensityRestriction);
     long numSpots = query.count(dc);
-    int normalizedSpots = 0;
+    long normalizedSpots = 0;
     if (progress != null) progress.display((int)(normalizedSpots / numSpots * 100), normalizedSpots + " spots normalized");
     
@@ -431 +431 @@
             }
             normalizedSpots += smoothCurve.size();
-            if (progress != null) progress.display((int)((normalizedSpots * 100) / numSpots), normalizedSpots + " spots normalized");
+            if (progress != null) progress.display((int)((normalizedSpots * 100L) / numSpots), normalizedSpots + " spots normalized");
           }
           fromBlock = toBlock + 1;

branches/2.5-stable/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java

@@ -349 +349 @@
     query.restrict(intensityRestriction);
     long numSpots = query.count(dc);
-    int normalizedSpots = 0;
+    long normalizedSpots = 0;
     if (progress != null) progress.display((int)(normalizedSpots / numSpots * 100), normalizedSpots + " spots normalized");
     
@@ -441 +441 @@
             }
             normalizedSpots += toIndex - fromIndex;
-            if (progress != null) progress.display((int)((normalizedSpots * 100) / numSpots), normalizedSpots + " spots normalized");
+            if (progress != null) progress.display((int)((normalizedSpots * 100L) / numSpots), normalizedSpots + " spots normalized");
           }
           fromBlock = toBlock + 1;