com.actelion.research.orbit.imageAnalysis.components.MetaTable Maven / Gradle / Ivy
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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2017 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see metaHash = new ConcurrentHashMap();
public MetaTable() {
addDefaultTable();
this.setPreferredSize(new Dimension(-1, 250));
}
private void addDefaultTable() {
// SwingUtilities.invokeLater(new Runnable() {
// @Override
// public void run() {
// Object[][] vals = new String[1][2];
// vals[0][0] = ""; vals[0][1] = "";
// JTable table = new JTable(vals, tableHeader);
// table.setCellEditor(new MetaCellEditor());
// MetaTable.this.add("Meta Data",table);
// }
// });
Object[][] vals = new String[1][2];
vals[0][0] = "";
vals[0][1] = "";
JTable table = new JTable(vals, tableHeader);
table.setCellEditor(new MetaCellEditor());
this.add("Meta Data", new JScrollPane(table));
}
public void clearMetas() {
removeAll();
addDefaultTable();
}
public void listRdfMetas(int rawDataFileId) {
try {
metaHash.clear();
List metaList = DALConfig.getImageProvider().LoadRawMetasByRawDataFile(rawDataFileId);
boolean descriptionAdded = false;
boolean commentAdded = false;
for (RawMeta rm : metaList) {
metaHash.put(rm.getName(), rm);
if (rm.getName().equals("Description")) descriptionAdded = true;
if (rm.getName().equals("Comment")) commentAdded = true;
}
RawDataFile rdf = DALConfig.getImageProvider().LoadRawDataFile(rawDataFileId);
RawMetaFactoryFile rmff = new RawMetaFactoryFile(rawDataFileId, new Date(), rdf.getUserId());
if (!descriptionAdded) {
RawMeta rm = rmff.createMetaStr("Description", "");
metaList.add(rm);
}
if (!commentAdded) {
RawMeta rm = rmff.createMetaStr("Comment", "");
metaList.add(rm);
}
listMetas(metaList);
} catch (Exception e) {
logger.error("error loading meta data", e);
}
}
public void listRawDataMetas(int rawDataId) {
try {
metaHash.clear();
List metaList = DALConfig.getImageProvider().LoadRawMetasByRawData(rawDataId);
for (RawMeta rm : metaList) {
metaHash.put(rm.getName(), rm);
}
listMetas(metaList);
} catch (Exception e) {
logger.error("error loading meta data", e);
}
}
/**
* Only called if DALConfig.isShowLIMSMetas()
*
* @param rdf
*/
public void listLIMSMetas(final RawDataFile rdf) {
metaHash.clear();
Thread t = new Thread(new Runnable() {
@Override
public void run() {
try {
RawMetaFactoryFile rmff = new RawMetaFactoryFile(rdf.getRawDataFileId(), new Date(), rdf.getUserId());
List rmList = DALConfig.getImageProvider().LoadRawMetasByRawDataFileAndName(rdf.getRawDataFileId(), RawUtilsCommon.STR_META_BARCODE);
if (rmList != null && rmList.size() > 0) {
String barcode = rmList.get(0).getValue();
if (barcode != null && barcode.length() > 0) {
barcode = barcode.trim();
List samples = DALConfig.getImageProvider().LoadByContainerId(barcode);
if (samples != null) {
for (LIMSBioSample sample : samples) {
List metaList = RawUtilsCommon.generateBiosampleMetas(sample, rmff);
for (RawMeta rm : metaList) {
metaHash.put(rm.getName(), rm);
}
listMetas(metaList);
}
}
}
}
} catch (Exception e) {
logger.info("error loading LIMS meta-data", e);
}
}
});
t.start();
}
private void listMetas(List metaList) {
//List metaList = DAORawMeta.LoadRawMetasByRawDataFile(rdf.getRawDataFileId());
// append with metas from rawData
//List rdMetas = DAORawMeta.LoadRawMetasByRawData(rdf.getRawDataId());
//for (RawMeta rm : rdMetas) {
// rm.setName("Container."+rm.getName());
//}
//metaList.addAll(rdMetas);
List> metaHash = RawMetaListBuilder.buildRawMetaHash(metaList);
this.removeAll();
int cnt = 0;
for (final ListWithName pGroup : metaHash) {
Object[][] tableData = new Object[pGroup.getList().size()][2];
for (int i = 0; i < pGroup.getList().size(); i++) {
cnt++;
RawMeta rm = pGroup.getList().get(i);
tableData[i][0] = rm;
tableData[i][1] = rm.getValueFormatted();
}
final TableModel tm = new MyEditableTableModel(tableData, tableHeader);
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
final JTable table = new JTable(tm);
if (OrbitUtils.DARKUI)
table.getColumnModel().getColumn(0).setCellRenderer(new MyMetaTableCellRendererSubstance());
else table.getColumnModel().getColumn(0).setCellRenderer(new MyMetaTableCellRendererNimbus());
table.getColumnModel().getColumn(1).setCellEditor(new MetaCellEditor());
MetaTable.this.add(pGroup.getName(), table);
}
});
}
}
public Map getMetaHash() {
return metaHash;
}
class MyEditableTableModel extends DefaultTableModel {
private static final long serialVersionUID = 1L;
public MyEditableTableModel() {
super();
}
public MyEditableTableModel(Object[][] data, Object[] columnNames) {
super(data, columnNames);
}
@Override
public boolean isCellEditable(int row, int column) {
return column > 0;
}
}
class MyMetaTableCellRendererNimbus extends DefaultTableCellRenderer.UIResource {
private static final long serialVersionUID = 1L;
public MyMetaTableCellRendererNimbus() {
super();
}
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
if (value instanceof RawMeta) {
RawMeta rm = (RawMeta) value;
return super.getTableCellRendererComponent(table, rm.getName(), isSelected, hasFocus, row, column);
} else
return super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
}
}
class MyMetaTableCellRendererSubstance extends SubstanceDefaultTableCellRenderer {
private static final long serialVersionUID = 1L;
public MyMetaTableCellRendererSubstance() {
super();
}
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
if (value instanceof RawMeta) {
RawMeta rm = (RawMeta) value;
return super.getTableCellRendererComponent(table, rm.getName(), isSelected, hasFocus, row, column);
} else
return super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
}
}
}