Fix for ccm and cmx out of sync

src/core/conditionaltest.cpp

@@ -47,10 +47,16 @@ std::unique_ptr<EAbstractAnalyticBlock> ConditionalTest::makeWork(int index) con
 
     // initialize pairwise iterator for cmx file
     CorrelationMatrix::Pair cmxPair(_cmx);
+    if (index == 0)
+    {
+        cmxPair.readFirst();
+    }
+    else
+    {
+        cmxPair.read(Pairwise::Index(start));
+    }
 
-    // iterate to the start index of the next work block
-    cmxPair.read(Pairwise::Index(start));
-
+    // Iterate to the start index of the next work block
     for ( qint64 i = 0; i < size; i++ )
     {
         cmxPair.readNext();
@@ -134,6 +140,7 @@ void ConditionalTest::process(const EAbstractAnalyticBlock* result)
         {
             csmPair.write(pair.index);
         }
+
     }
 }
 

src/core/conditionaltest_serial.cpp

@@ -57,10 +57,12 @@ std::unique_ptr<EAbstractAnalyticBlock> ConditionalTest::Serial::execute(const E
     // iterate through each pair in the work block
     for ( qint64 wbIndex = 0; wbIndex < workBlock->size(); ++wbIndex )
     {
+
         // print warning if iterator indices do not match
         if ( ccmPair.index() != cmxPair.index() )
         {
-            qInfo() << "warning: ccm and cmx files are out of sync";
+            qInfo() << "warning: ccm and cmx files are out of sync at cmx coordinate ("
+                    << cmxPair.index().getX() << "," << cmxPair.index().getY() <<").";
         }
 
         // initialize set of p values and r2 values for each cluster
@@ -117,14 +119,14 @@ std::unique_ptr<EAbstractAnalyticBlock> ConditionalTest::Serial::execute(const E
 
         // append pair to result block
         resultBlock->append(Pair {
-            ccmPair.index(),
+            cmxPair.index(),
             pValues,
             r2
         });
 
         // read the next pair
-        ccmPair.readNext();
         cmxPair.readNext();
+        ccmPair.read(cmxPair.index());
     }
 
     return std::unique_ptr<EAbstractAnalyticBlock>(resultBlock);
@@ -422,7 +424,6 @@ void ConditionalTest::Serial::test_proportions (
     {
         // Keeps track of the number of successes for each iteration.
         int ns = 0;
-        int fs = 0;
 
         // The gsl_ran_sample function randomly chooses samples with replacement from a list.
         int chosen[bs_t];
@@ -431,7 +432,6 @@ void ConditionalTest::Serial::test_proportions (
         // Now count the number of randomly selected items from the cluster.
         for ( int j = 0; j < bs_t; j++ )
         {
-            int etype = ccmPair.at(clusterIndex, chosen[j]);
             QString slabel = amx_column.at(chosen[j]);
             if ( ccmPair.at(clusterIndex, chosen[j]) == 1 && amx_column.at(chosen[j]) == test_label )
             {

src/core/corrpower.cpp

@@ -47,10 +47,16 @@ std::unique_ptr<EAbstractAnalyticBlock> CorrPowerFilter::makeWork(int index) con
 
     // initialize pairwise iterator for cmx file
     CorrelationMatrix::Pair cmxPair(_cmx);
+    if (index == 0)
+    {
+        cmxPair.readFirst();
+    }
+    else
+    {
+        cmxPair.read(Pairwise::Index(start));
+    }
 
-    // iterate to the start index of the next work block
-    cmxPair.read(Pairwise::Index(start));
-
+    // Iterate to the start index of the next work block
     for ( qint64 i = 0; i < size; i++ )
     {
         cmxPair.readNext();
@@ -59,6 +65,7 @@ std::unique_ptr<EAbstractAnalyticBlock> CorrPowerFilter::makeWork(int index) con
     // save start index of next work block
     _workBlockStart = cmxPair.index().toRawIndex();
 
+
     // construct work block
     return std::unique_ptr<EAbstractAnalyticBlock>(new WorkBlock(index, start, size));
 }

src/core/corrpower_serial.cpp

@@ -59,10 +59,12 @@ std::unique_ptr<EAbstractAnalyticBlock> CorrPowerFilter::Serial::execute(const E
     // Iterate through each pair in the work block.
     for ( qint64 wbIndex = 0; wbIndex < workBlock->size(); ++wbIndex )
     {
+
         // Print warning if iterator indices do not match
         if ( ccmPair.index() != cmxPair.index() )
         {
-            qInfo() << "warning: ccm and cmx files are out of sync";
+            qInfo() << "warning: ccm and cmx files are out of sync at cmx coordinate ("
+                    << cmxPair.index().getX() << "," << cmxPair.index().getY() <<").";
         }
 
         // Get the number of samples and clusters.
@@ -128,16 +130,17 @@ std::unique_ptr<EAbstractAnalyticBlock> CorrPowerFilter::Serial::execute(const E
         if ( new_correlations.size() > 0 )
         {
             resultBlock->append(Pair {
-                ccmPair.index(),
+                cmxPair.index(),
                 new_labels,
                 new_correlations,
                 k_keep
             });
         }
 
         // read the next pair
-        ccmPair.readNext();
         cmxPair.readNext();
+        ccmPair.read(cmxPair.index());
+
     }
 
     // We're done! Return the result block.

src/core/extract_networkwriter.cpp

@@ -44,28 +44,36 @@ int Extract::NetworkWriter::readNext()
 {
     EDEBUG_FUNC(this,cmx_index);
 
-    // read the next pair in the cmx
-    _cmxPair.readNext();
+    // Read the next pair in the cmx.
+    if(_cmxPair.index().toRawIndex() == 0)
+    {
+        _cmxPair.readFirst();
+    }
+    else {
+        _cmxPair.readNext();
+    }
 
     // read the next pair in the ccm (should always match cmx)
     if ( _ccm )
     {
-        _ccmPair.readNext();
+        _ccmPair.read(_cmxPair.index());
 
         if ( _cmxPair.index() != _ccmPair.index() )
         {
-            qInfo() << "warning: cmx and ccm are out of sync";
+            qInfo() << "warning: cmx and ccm are out of sync at cmx coordinate ("
+                    << _cmxPair.index().getX() << "," << _cmxPair.index().getY() <<").";
         }
     }
 
     // read the next pair in the csm (should always match cmx)
     if ( _csm )
     {
-        _csmPair.readNext();
+        _csmPair.read(_cmxPair.index());
 
         if ( _cmxPair.index() != _csmPair.index() )
         {
-            qInfo() << "warning: cmx and ccm are out of sync";
+            qInfo() << "warning: cmx and ccm are out of sync at cmx coordinate ("
+                    << _cmxPair.index().getX() << "," << _cmxPair.index().getY() <<").";
         }
     }
 

src/core/pairwise_matrix_pair.cpp

@@ -44,8 +44,10 @@ void Matrix::Pair::write(const Index& index)
  * Read the pair with the given pairwise index from the data object file.
  *
  * @param index
+ *
+ * @return the index of the pair. If no pair is found at this index then -1 is returned.
  */
-void Matrix::Pair::read(const Index& index) const
+qint64 Matrix::Pair::read(const Index& index) const
 {
     EDEBUG_FUNC(this,&index);
 
@@ -61,10 +63,30 @@ void Matrix::Pair::read(const Index& index) const
         _rawIndex = clusterIndex;
         readNext();
     }
+    return clusterIndex;
+
 }
 
 
 
+/*!
+ * For sparse matricies the index of the first pair may not be know.
+ *
+ * This function is used to find that first pair and read it.
+ */
+void Matrix::Pair::readFirst() const
+{
+    EDEBUG_FUNC(this);
+
+    for (qint64 i = 0; i < _cMatrix->size(); i++)
+    {
+        if (this->read(Pairwise::Index(i)) != -1) {
+            return;
+        }
+    }
+}
+
+
 /*!
  * Read the next pair in the data object file.
  */

src/core/pairwise_matrix_pair.h

@@ -32,8 +32,9 @@ namespace Pairwise
         virtual int clusterSize() const = 0;
         virtual bool isEmpty() const = 0;
         void write(const Index& index);
-        void read(const Index& index) const;
+        qint64 read(const Index& index) const;
         void reset() const { _rawIndex = 0; }
+        void readFirst() const;
         void readNext() const;
         bool hasNext() const { return _rawIndex != _cMatrix->_clusterSize; }
         const Index& index() const { return _index; }