/* Copyright (c) 2007-2009 The University of the West Indies * * Contact: robert.lancashire@uwimona.edu.jm * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public * License as published by the Free Software Foundation; either * version 2.1 of the License, or (at your option) any later version. * * This library 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 * Lesser General License for more details. * * You should have received a copy of the GNU Lesser General Public * License along with this library; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */ package jspecview.source; import java.io.BufferedReader; import java.io.IOException; import javajs.util.Base64; import javajs.util.BC; /** * Representation of a XML Source. * @author Craig A.D. Walters * @author Prof. Robert J. Lancashire */ public class AnIMLReader extends XMLReader { public AnIMLReader() { // called by reflection from FileReader } @Override protected JDXSource getXML(BufferedReader br) { try { source = new JDXSource(JDXSource.TYPE_SIMPLE, filePath); getSimpleXmlReader(br); parser.nextEvent(); processXML(AML_0, AML_1); if (!checkPointCount()) return null; xFactor = 1; yFactor = 1; populateVariables(); } catch (Exception pe) { System.err.println("That file may be empty..."); errorLog.append("That file may be empty... \n"); } processErrors("anIML"); try { br.close(); } catch (IOException e1) { // } return source; } /** * Process the XML events. * Invoked for every start tag. * * Invoked by the superclass method * XMLSource.process(tagId, requiresEndTag) * * @param tagId * @return true to continue looking for encapsulated tags * false to process once only (no encapsulated tags of interest) * @throws Exception */ @Override protected boolean processTag(int tagId) throws Exception { switch (tagId) { case AML_AUDITTRAIL: processAuditTrail(); return true; case AML_EXPERIMENTSTEPSET: processExperimentStepSet(); return true; case AML_SAMPLESET: processSampleSet(); return true; case AML_AUTHOR: // AML_AUTHOR is processed via AML_EXPERIMENTSTEPSET processAuthor(); return true; case AML_RESULT: inResult = true; return true; default: System.out.println("AnIMLReader not processing tag " + tagNames[tagId]); // should not be here return false; } } @Override protected void processEndTag(int tagId) throws Exception { switch(tagId) { case AML_RESULT: case AML_EXPERIMENTSTEPSET: inResult = false; break; } } private void processAuditTrail() throws Exception { if (tagName.equals("user")) { parser.qualifiedValue(); } else if (tagName.equals("timestamp")) { parser.qualifiedValue(); } } private void processSampleSet() throws Exception { if (tagName.equals("sample")) samplenum++; else if (tagName.equals("parameter")) { attrList = parser.getAttrValueLC("name"); if (attrList.equals("name")) { parser.qualifiedValue(); } else if (attrList.equals("owner")) { parser.qualifiedValue(); } else if (attrList.equals("molecular formula")) { molForm = parser.qualifiedValue(); } else if (attrList.equals("cas registry number")) { casRN = parser.qualifiedValue(); } } } private boolean inResult; private void processExperimentStepSet() throws Exception { if (tagName.equals("result")) { inResult = true; } else if (tagName.equals("sampleref")) { if (parser.getAttrValueLC("role").contains("samplemeasurement")) sampleID = parser.getAttrValue("sampleID"); } else if (tagName.equals("author")) { process(AML_AUTHOR, true); } else if (tagName.equals("timestamp")) { LongDate = parser.thisValue(); } else if (tagName.equals("technique")) { techname = parser.getAttrValue("name").toUpperCase() + " SPECTRUM"; } else if (tagName.equals("vectorset") || tagName.equals("seriesset") && inResult) { npoints = Integer.parseInt(parser.getAttrValue("length")); //System.out.println("AnIML No. of points= " + npoints); xaxisData = new double[npoints]; yaxisData = new double[npoints]; } else if (tagName.equals("vector") || tagName.equals("series") && inResult) { String axisLabel = parser.getAttrValue("name"); String dependency = parser.getAttrValueLC("dependency"); if (dependency.equals("independent")) { xUnits = axisLabel; getXValues(); } else if (dependency.equals("dependent")) { yUnits = axisLabel; getYValues(); } } else if (tagName.equals("parameter")) { if ((attrList = parser.getAttrValueLC("name")).equals("identifier")) { title = parser.qualifiedValue(); } else if (attrList.equals("nucleus")) { obNucleus = parser.qualifiedValue(); } else if (attrList.equals("observefrequency")) { StrObFreq = parser.qualifiedValue(); obFreq = Double.parseDouble(StrObFreq); } else if (attrList.equals("referencepoint")) { refPoint = Double.parseDouble(parser.qualifiedValue()); } else if (attrList.equals("sample path length")) { pathlength = parser.qualifiedValue(); } else if (attrList.equals("scanmode")) { parser.thisValue(); // ignore? } else if (attrList.equals("manufacturer")) { vendor = parser.thisValue(); } else if (attrList.equals("model name")) { modelType = parser.thisValue(); } else if (attrList.equals("resolution")) { resolution = parser.qualifiedValue(); } } } private void getXValues() throws Exception { parser.nextTag(); if (parser.getTagName().equals("autoincrementedvalueset")) { parser.nextTag(); if (parser.getTagName().equals("startvalue")) firstX = Double.parseDouble(parser.qualifiedValue()); nextStartTag(); if (parser.getTagName().equals("increment")) deltaX = Double.parseDouble(parser.qualifiedValue()); } if (!inResult) { nextStartTag(); xUnits = parser.getAttrValue("label"); } increasing = (deltaX > 0 ? true : false); continuous = true; for (int j = 0; j < npoints; j++) xaxisData[j] = firstX + (deltaX * j); lastX = xaxisData[npoints - 1]; } private void nextStartTag() throws Exception { parser.nextStartTag(); while (parser.getTagType() == XMLParser.COMMENT) { parser.nextStartTag(); } } private void getYValues() throws Exception { String vectorType = parser.getAttrValueLC("type"); if (vectorType.length() == 0) vectorType = parser.getAttrValueLC("vectorType"); parser.nextTag(); tagName = parser.getTagName(); if (tagName.equals("individualvalueset")) { for (int ii = 0; ii < npoints; ii++) yaxisData[ii] = Double.parseDouble(parser.qualifiedValue()); //System.out.println(npoints + " individual Y values now read"); } else if (tagName.equals("encodedvalueset")) { attrList = parser.getCharacters(); byte[] dataArray = Base64.decodeBase64(attrList); if (dataArray.length != 0) { if (vectorType.equals("float64")) { for (int i = 0, pt = 0; i < npoints; i++, pt += 8) yaxisData[i] = BC.bytesToDoubleToFloat(dataArray, pt, false); } else { for (int i = 0, pt = 0; i < npoints; i++, pt += 4) yaxisData[i] = BC.bytesToFloat(dataArray, pt, false); } } } parser.nextStartTag(); tagName = parser.getTagName(); yUnits = parser.getAttrValue("label"); firstY = yaxisData[0]; } private void processAuthor() throws Exception { if (tagName.equals("name")) owner = parser.thisValue(); else if (tagName.contains("location")) origin = parser.thisValue(); } }