diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index 18327b53c5c0975d7c454322981a82ce22277fb8..de46beff3ff0896becaf2a172d1d222d624cf377 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -47,6 +47,10 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
private IEncapsulatedOpenBISService openBisService;
+ final public static String WELL_ROW_COLUMN = "Row";
+
+ final public static String WELL_COLUMN_COLUMN = "Column";
+
/**
* An CSV-file-like interface to feature data from the database.
*
@@ -56,10 +60,6 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
{
private static final String WELL_NAME_COLUMN = "WellName";
- private static final String WELL_ROW_COLUMN = "Row";
-
- private static final String WELL_COLUMN_COLUMN = "Column";
-
private final IImagingQueryDAO dao;
private final IEncapsulatedOpenBISService service;
@@ -67,7 +67,7 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
private final String dataSetCode;
private String[] headerCodes;
-
+
private String[] headerLabels;
private ArrayList<String[]> lines;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/SpreadsheetColumnTickUnit.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/SpreadsheetColumnTickUnit.java
new file mode 100644
index 0000000000000000000000000000000000000000..b5c0e8682de754ad14a54e7e765185c426e0277d
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/SpreadsheetColumnTickUnit.java
@@ -0,0 +1,67 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.server.graph;
+
+import org.jfree.chart.axis.NumberTickUnit;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class SpreadsheetColumnTickUnit extends NumberTickUnit
+{
+ private static final long serialVersionUID = 1L;
+
+ // Note: this should work as a way of letting the axis select the appropriate
+ // tick interval, but it doesn't work for some reason.
+ //
+ // public static TickUnitSource createStandardTickUnits()
+ // {
+ // TickUnits tickUnits = new TickUnits();
+ // tickUnits.add(new SpreadsheetColumnTickUnit(1.0));
+ // tickUnits.add(new SpreadsheetColumnTickUnit(2.0));
+ // tickUnits.add(new SpreadsheetColumnTickUnit(5.0));
+ // return tickUnits;
+ // }
+
+ /**
+ * Constructor for a spreadsheet tick unit label.
+ */
+ public SpreadsheetColumnTickUnit(double size)
+ {
+ super(size);
+ }
+
+ /**
+ * Converts the supplied value to a string.
+ * <P>
+ * Subclasses may implement special formatting by overriding this method.
+ *
+ * @param value the data value.
+ * @return Value as string.
+ */
+ @Override
+ public String valueToString(double value)
+ {
+ if (value < 1)
+ {
+ return "";
+ }
+ return PlateUtils.translateRowNumberIntoLetterCode((int) value);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
index 84d3f1ba72c3d5ea9cef05e8c433c7282c23225c..36fb739e6f57ed6159076145851c1bd2d2008cdb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataGraphCollectionConfiguration.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.utilities.PropertyParametersUtil;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.common.utilities.PropertyParametersUtil.SectionProperties;
+import ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet;
import ch.systemsx.cisd.openbis.dss.generic.server.graph.TabularDataGraphConfiguration.GraphType;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabel;
@@ -177,8 +178,14 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
switch (type)
{
case HEATMAP:
- CodeAndLabel xAxis = getCodeAndLabel(props, X_AXIS_KEY);
- CodeAndLabel yAxis = getCodeAndLabel(props, Y_AXIS_KEY);
+ // Default the Row and Column header names to the standard ones if no override is
+ // specified.
+ CodeAndLabel xAxis =
+ getCodeAndLabelWithDefault(props, X_AXIS_KEY,
+ TabularDataGraphServlet.WELL_ROW_COLUMN);
+ CodeAndLabel yAxis =
+ getCodeAndLabelWithDefault(props, Y_AXIS_KEY,
+ TabularDataGraphServlet.WELL_ROW_COLUMN);
CodeAndLabel zAxis = getCodeAndLabel(props, COLUMN_KEY);
if (xAxis.equals(yAxis))
{
@@ -203,7 +210,7 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
// should never get here
return null;
}
-
+
private CodeAndLabel getCodeAndLabel(Properties properties, String key)
{
String labelWithOptionalCode = properties.getProperty(key);
@@ -227,6 +234,30 @@ public class TabularDataGraphCollectionConfiguration implements ICsvFileReaderCo
return new CodeAndLabel(code, label);
}
+ private CodeAndLabel getCodeAndLabelWithDefault(Properties properties, String key,
+ String defaultLabel)
+ {
+ String labelWithOptionalCode = properties.getProperty(key);
+ if (labelWithOptionalCode != null)
+ {
+ return new CodeAndLabel(labelWithOptionalCode);
+ }
+ String labelKey = key + LABEL_POSTFIX;
+ String label = properties.getProperty(labelKey);
+ String codeKey = key + CODE_POSTFIX;
+ String code = properties.getProperty(codeKey);
+ if (label == null && code == null)
+ {
+ label = defaultLabel;
+ code = CodeAndLabel.normalize(label);
+ }
+ if (code == null)
+ {
+ return new CodeAndLabel(label);
+ }
+ return new CodeAndLabel(code, label);
+ }
+
/**
* Return the graph configuration associated with the graphTypeCode.
*
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
index 74c322f9cc9c9fbbf9d29e6e338cfa824715eeae..8565bc3f61d48a05ae587c9138807028e2c8479c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmap.java
@@ -24,7 +24,6 @@ import java.util.List;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
-import org.jfree.chart.axis.NumberTickUnit;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.LookupPaintScale;
@@ -48,6 +47,8 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ITabularData;
public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeatmapConfiguration>
{
+ private static final int PAINT_SCALE_NUM_STEPS = 11;
+
/**
* @param configuration
*/
@@ -107,7 +108,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
throw new IllegalArgumentException("Null 'orientation' argument.");
}
NumberAxis xAxis = new NumberAxis(xAxisLabel);
- xAxis.setTickUnit(new NumberTickUnit(1.0));
+ xAxis.setTickUnit(new SpreadsheetColumnTickUnit(1.0));
xAxis.setInverted(true);
NumberAxis yAxis = new NumberAxis(yAxisLabel);
@@ -130,6 +131,9 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
NumberAxis scaleAxis = new NumberAxis("Scale");
scaleAxis.setRange(dataset.getRange());
scaleAxis.setStandardTickUnits(new TabularDataTickUnitSource());
+ scaleAxis.setTickUnit(new TabularDataTickUnit(dataset.getRange().getLength()
+ / PAINT_SCALE_NUM_STEPS));
+ scaleAxis.setAutoRange(true);
PaintScaleLegend psl = new PaintScaleLegend(paintScale, scaleAxis);
psl.setMargin(new RectangleInsets(5, 5, 5, 5));
psl.setPosition(RectangleEdge.RIGHT);
@@ -160,7 +164,7 @@ public class TabularDataHeatmap extends AbstractTabularDataGraph<TabularDataHeat
LookupPaintScale paintScale = new LookupPaintScale(lowerBound, upperBound, Color.WHITE);
double binMin = range.getLowerBound();
- double binStep = range.getLength() / 11;
+ double binStep = range.getLength() / PAINT_SCALE_NUM_STEPS;
// 1
paintScale.add(binMin, new Color(5, 48, 97));
// 2
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnit.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnit.java
new file mode 100644
index 0000000000000000000000000000000000000000..f922a2f021ec270ef4b0cfd663516cc9c85293d0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnit.java
@@ -0,0 +1,104 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.server.graph;
+
+import java.text.DecimalFormat;
+
+import org.jfree.chart.axis.NumberTickUnit;
+
+/**
+ * This is a variation on the NumberTickUnit that gracefully switches from standard to scientific
+ * notation depending on the size of the numbers for the labels.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class TabularDataTickUnit extends NumberTickUnit
+{
+ private static final long serialVersionUID = 1L;
+
+ final private static int largeScientificNotationTransition = 6;
+
+ final private static int smallScientificNotationTransition = 3;
+
+ /**
+ * @param size
+ */
+ public TabularDataTickUnit(double size)
+ {
+ super(size, getNumberFormat(Math.abs(size), size >= 1.0));
+ }
+
+ /**
+ * Use the precision to determine if we should return standard or scientific notation.
+ *
+ * @param precision The desired precision of the numbers to display.
+ * @param greaterThan1 True if the numbers to be shown are greater then 1
+ */
+ private static DecimalFormat getNumberFormat(double precision, boolean greaterThan1)
+ {
+ DecimalFormat numberFormat;
+ if (greaterThan1)
+ {
+ if (precision > largeScientificNotationTransition)
+ {
+ numberFormat = new DecimalFormat("0.0##E0");
+ } else
+ {
+ numberFormat = getStandardNumberFormat((int) precision, greaterThan1);
+ }
+ } else
+ {
+ if (precision > smallScientificNotationTransition)
+ {
+ numberFormat = new DecimalFormat("0.0##E0");
+ } else
+ {
+ numberFormat = getStandardNumberFormat((int) precision, greaterThan1);
+ }
+ }
+ return numberFormat;
+ }
+
+ /**
+ * Return a DecimalFormat that uses standard notation (not scientific notation).
+ *
+ * @param precision The desired precision of the numbers to display.
+ * @param greaterThan1 True if the numbers to be shown are greater then 1
+ */
+ private static DecimalFormat getStandardNumberFormat(int precision, boolean greaterThan1)
+ {
+ StringBuilder sb = new StringBuilder();
+ if (greaterThan1)
+ {
+ for (int i = 1; i < precision; ++i)
+ {
+ sb.append("#");
+ }
+ sb.append("0");
+ } else
+ {
+ sb.append("0.0");
+ for (int i = 0; i < precision - 1; ++i)
+ {
+ sb.append("0");
+ }
+ }
+
+ return new DecimalFormat(sb.toString());
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnitSource.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnitSource.java
index 657a0671bfdade1d717ecba73c787fd7677f236a..6215fea85c9e25883ebc03023af801556bf3f722 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnitSource.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataTickUnitSource.java
@@ -17,9 +17,7 @@
package ch.systemsx.cisd.openbis.dss.generic.server.graph;
import java.io.Serializable;
-import java.text.DecimalFormat;
-import org.jfree.chart.axis.NumberTickUnit;
import org.jfree.chart.axis.TickUnit;
import org.jfree.chart.axis.TickUnitSource;
@@ -39,10 +37,6 @@ public class TabularDataTickUnitSource implements TickUnitSource, Serializable
/** Constant for log(10.0). */
final private static double LOG_10_VALUE = Math.log(10.0);
- final private int largeScientificNotationTransition = 6;
-
- final private int smallScientificNotationTransition = 3;
-
/**
* Returns a tick unit that is larger than the supplied unit.
*
@@ -75,75 +69,12 @@ public class TabularDataTickUnitSource implements TickUnitSource, Serializable
*/
public TickUnit getCeilingTickUnit(double size)
{
- // Use number of decimal digits to determine what the tick size and display format should
- // be.
final double numberOfDigits = Math.log(size) / LOG_10_VALUE;
final double higher = Math.ceil(numberOfDigits);
- final DecimalFormat numberFormat = getNumberFormat(Math.abs(higher), size >= 1.0);
final double fullTickIncrement = Math.pow(10, higher);
final double halfTickIncrement = fullTickIncrement / 2;
final double tickIncrement =
(size <= halfTickIncrement) ? halfTickIncrement : fullTickIncrement;
- return new NumberTickUnit(tickIncrement, numberFormat);
- }
-
- /**
- * Use the precision to determine if we should return standard or scientific notation.
- *
- * @param precision The desired precision of the numbers to display.
- * @param greaterThan1 True if the numbers to be shown are greater then 1
- */
- private DecimalFormat getNumberFormat(double precision, boolean greaterThan1)
- {
- DecimalFormat numberFormat;
- if (greaterThan1)
- {
- if (precision > largeScientificNotationTransition)
- {
- numberFormat = new DecimalFormat("0.0##E0");
- } else
- {
- numberFormat = getStandardNumberFormat((int) precision, greaterThan1);
- }
- } else
- {
- if (precision > smallScientificNotationTransition)
- {
- numberFormat = new DecimalFormat("0.0##E0");
- } else
- {
- numberFormat = getStandardNumberFormat((int) precision, greaterThan1);
- }
- }
- return numberFormat;
- }
-
- /**
- * Return a DecimalFormat that uses standard notation (not scientific notation).
- *
- * @param precision The desired precision of the numbers to display.
- * @param greaterThan1 True if the numbers to be shown are greater then 1
- */
- private DecimalFormat getStandardNumberFormat(int precision, boolean greaterThan1)
- {
- StringBuilder sb = new StringBuilder();
- if (greaterThan1)
- {
- for (int i = 1; i < precision; ++i)
- {
- sb.append("#");
- }
- sb.append("0");
- } else
- {
- sb.append("0.0");
- for (int i = 0; i < precision - 1; ++i)
- {
- sb.append("0");
- }
- }
-
- return new DecimalFormat(sb.toString());
-
+ return new TabularDataTickUnit(tickIncrement);
}
}