Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java

@@ -26,7 +26,9 @@ package org.broadinstitute.sting.gatk.report;
 
 import org.apache.commons.lang.math.NumberUtils;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.LinkedHashMap;
 
 /**
  * Holds values for a column in a GATK report table
@@ -38,6 +40,10 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
     final private boolean display;
     final private GATKReportDataType dataType;
 
+    private GATKReportColumnFormat columnFormat;
+    private GATKReportColumnFormat.Alignment alignment = GATKReportColumnFormat.Alignment.RIGHT;                        // default alignment is to the right unless values added ask for a left alignment
+    private int maxWidth = 0;
+
     /**
      * Construct the column object, specifying the column name, default value, whether or not the column should be
      * displayed, and the format string. This cannot be null.
@@ -49,6 +55,7 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
      */
     public GATKReportColumn(String columnName, Object defaultValue, boolean display, String format) {
         this.columnName = columnName;
+        this.maxWidth = columnName.length();
         this.display = display;
         if ( format.equals("") ) {
             this.format = "%s";
@@ -85,7 +92,8 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
 
     /**
      * Return an object from the column, but if it doesn't exist, return the default value.  This is useful when writing
-     * tables, as the table gets written properly without having to waste storage for the unset elements (usually the zero
+     * tables, as the table gets written properly without having to waste storage for the unset elements (usually the
+     * zero
      * values) in the table.
      *
      * @param primaryKey the primary key position in the column that should be retrieved
@@ -120,32 +128,17 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
     }
 
     /**
-     * Get the display width for this column.  This allows the entire column to be displayed with the appropriate, fixed width.
+     * Get the display width for this column.  This allows the entire column to be displayed with the appropriate, fixed
+     * width.
      *
      * @return the format string for this column
      */
     public GATKReportColumnFormat getColumnFormat() {
-        int maxWidth = columnName.length();
+        if (columnFormat != null)
-        GATKReportColumnFormat.Alignment alignment = GATKReportColumnFormat.Alignment.RIGHT;
+            return columnFormat;
 
-        for (Object obj : this.values()) {
+        columnFormat = new GATKReportColumnFormat(maxWidth, alignment);
-            if (obj != null) {
+        return columnFormat;
-                String formatted = formatValue(obj);
-
-                int width = formatted.length();
-                if (width > maxWidth) {
-                    maxWidth = width;
-                }
-
-                if (alignment == GATKReportColumnFormat.Alignment.RIGHT) {
-                    if (!isRightAlign(formatted)) {
-                        alignment = GATKReportColumnFormat.Alignment.LEFT;
-                    }
-                }
-            }
-        }
-
-        return new GATKReportColumnFormat(maxWidth, alignment);
     }
 
     private static final Collection<String> RIGHT_ALIGN_STRINGS = Arrays.asList(
@@ -176,10 +169,11 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
         String value;
         if (obj == null) {
             value = "null";
-        } else if ( dataType.equals(GATKReportDataType.Unknown) &&
+        }
-                (obj instanceof Double || obj instanceof Float) ) {
+        else if ( dataType.equals(GATKReportDataType.Unknown) && (obj instanceof Double || obj instanceof Float) ) {
             value = String.format("%.8f", obj);
-        } else
+        }
+        else
             value = String.format(format, obj);
 
         return value;
@@ -226,4 +220,23 @@ public class GATKReportColumn extends LinkedHashMap<Object, Object> {
         else
             return format;
     }
+
+    @Override
+    public Object put(Object key, Object value) {
+        if (value != null) {
+            String formatted = formatValue(value);
+            updateMaxWidth(formatted);
+            updateFormat(formatted);
+        }
+        return super.put(key, value);        
+    }
+
+    private void updateMaxWidth(String formatted) {
+        maxWidth = Math.max(formatted.length(), maxWidth);
+    }
+
+    private void updateFormat(String formatted) {
+        if (!isRightAlign(formatted))
+            alignment = GATKReportColumnFormat.Alignment.LEFT;
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java

@@ -405,7 +405,7 @@ public class GATKReportTable {
     public void set(Object primaryKey, String columnName, Object value) {
         verifyEntry(primaryKey, columnName);
         GATKReportColumn column = columns.get(columnName);
-        // Check if value is of same type as column
+        //todo -- Check if value is of same type as column
 
         // We do not accept internal null values
         if (value == null)
@@ -422,17 +422,18 @@ public class GATKReportTable {
                 try {
                     newValue = Long.parseLong((String) value);
                 } catch (Exception e) {
+                    /** do nothing */
                 }
             }
             if (column.getDataType().equals(GATKReportDataType.Decimal)) {
                 try {
                     newValue = Double.parseDouble((String) value);
                 } catch (Exception e) {
+                    /** do nothing */
                 }
             }
             if (column.getDataType().equals(GATKReportDataType.Character) && ((String) value).length() == 1) {
                 newValue = ((String) value).charAt(0);
-
             }
         }
 
@@ -900,13 +901,10 @@ public class GATKReportTable {
     public boolean isSameFormat(GATKReportTable table) {
         //Should we add the sortByPrimaryKey as a check?
 
-        if (!columns.isSameFormat(table.columns)) {
+        return columns.isSameFormat(table.columns) &&
-            return false;
+               (primaryKeyDisplay == table.primaryKeyDisplay && primaryKeyName.equals(table.primaryKeyName) &&
-        }
+               tableName.equals(table.tableName) &&
-        return (primaryKeyDisplay == table.primaryKeyDisplay &&
+               tableDescription.equals(table.tableDescription));
-                primaryKeyName.equals(table.primaryKeyName) &&
-                tableName.equals(table.tableName) &&
-                tableDescription.equals(table.tableDescription));
     }
 
     /**
@@ -916,12 +914,10 @@ public class GATKReportTable {
      * @return true if all field in the reports, tables, and columns are equal.
      */
     public boolean equals(GATKReportTable table) {
-        if (!isSameFormat(table)) {
+        return isSameFormat(table) &&
-            return false;
+               (columns.equals(table.columns) &&
-        }
+               primaryKeyColumn.equals(table.primaryKeyColumn) &&
-        return (columns.equals(table.columns) &&
+               sortByPrimaryKey == table.sortByPrimaryKey);
-                primaryKeyColumn.equals(table.primaryKeyColumn) &&
-                sortByPrimaryKey == table.sortByPrimaryKey);
 
     }
 }