adding a general utility package for Java or JavaScript.
--- /dev/null
+package javajs;
+
+public @interface J2SIgnoreImport {
+
+ Class<?>[] value();
+
+}
--- /dev/null
+package javajs;
+
+public @interface J2SRequireImport {
+
+ Class<?>[] value();
+
+}
--- /dev/null
+The javajs directory contains a variety of Java files that you are
+encouraged to use in your project. It is self-contained, and the
+classes and methods all work in Java as well as JavaScript.
+
+These classes perform functions not standard in Java or provide
+classes that are particularly optimized for JavaScript (fewer overloaded
+methods, especially).
+
+-- creating (minimal) PDF files
+-- decoding and encoding image files
+-- working with binary, compound document, JSON, and zip data
+-- providing very efficient classes for vectors, matricies, and quaternions
+-- providing a java.lang.Thread subclass (JSThread) that can be used
+ wherever a thread is necessary; note that JSThread cannot sleep(), but
+ it provides a means of managing setTimeout callbacks that is very easy
+ to implement.
+-- providing two very important annotations:
+
+ @J2SIgnoreImport Indicates that this class will never be used in JavaScript
+ and thus does not need to be indicated as a dependency. In
+ some cases, this annotation is necessary just to break a
+ cyclical dependency that Java somehow handles, but J2S does not.
+
+ @J2SRequireImport Allows a SwingJS developer to work around J2S transpiler
+ issues that for some reason it is not indicating the need for
+ a dependent class. Typically this is because a static call
+ to a static method in a class.
+
+ In addition, though, @J2SRequireImport can be used to "inject"
+ JavaScript at a specific point in code loading. For example,
+ swingjs.plaf.JSSlider uses the following annotation to load
+ jQueryUI, fooling J2S to think that it is a "class" file.
+
+ @J2SRequireImport(swingjs.jquery.JQueryUI.class)
+
+
+All files in the javajs/util directory will be moved to j2s/JU by a build script.
+
--- /dev/null
+package javajs.api;
+
+public interface BytePoster {
+
+ String postByteArray(String fileName, byte[] bytes);
+
+}
--- /dev/null
+package javajs.api;
+
+import javajs.util.V3;
+
+public interface EigenInterface {
+
+ EigenInterface setM(double[][] n);
+
+ double[] getEigenvalues();
+
+ void fillFloatArrays(V3[] eigenVectors, float[] eigenValues);
+
+ float[][] getEigenvectorsFloatTransposed();
+
+}
--- /dev/null
+package javajs.api;
+
+import java.io.BufferedInputStream;
+import java.io.DataInputStream;
+import java.io.InputStream;
+import java.util.Map;
+
+
+import javajs.util.SB;
+
+public interface GenericBinaryDocument extends GenericBinaryDocumentReader {
+
+ GenericBinaryDocument setStream(BufferedInputStream bis, boolean isBigEndian);
+
+ void setStreamData(DataInputStream dataInputStream, boolean isBigEndian);
+
+ long getPosition();
+
+ SB getAllDataFiles(String binaryFileList, String firstFile);
+
+ void getAllDataMapped(String replace, String string, Map<String, String> fileData);
+
+ int swapBytesI(int nx);
+
+ short swapBytesS(short s);
+
+ void seek(long i);
+
+ void setOutputChannel(GenericOutputChannel out);
+
+ InputStream getInputStream();
+
+ int readIntLE() throws Exception;
+
+ int readByteArray(byte[] b, int off, int len) throws Exception;
+
+
+ void close();
+
+}
--- /dev/null
+package javajs.api;
+
+public interface GenericBinaryDocumentReader {
+
+ byte readByte() throws Exception;
+
+ byte[] readBytes(int n) throws Exception;
+
+ int readUInt8() throws Exception;
+
+ int readInt() throws Exception;
+
+ short readShort() throws Exception;
+
+ int readUnsignedShort() throws Exception;
+
+ long readLong() throws Exception;
+
+ float readFloat() throws Exception;
+
+ double readDouble() throws Exception;
+
+ String readString(int i) throws Exception;
+
+}
--- /dev/null
+package javajs.api;
+
+import java.io.BufferedReader;
+import java.util.Map;
+
+
+public interface GenericCifDataParser {
+
+ static final int NONE = -1;
+
+ String fullTrim(String str);
+
+ Map<String, Object> getAllCifData();
+
+ boolean getData() throws Exception;
+
+ String getColumnName(int i);
+
+ int getColumnCount();
+
+ String getFileHeader();
+
+ Object peekToken() throws Exception;
+
+ Object getTokenPeeked();
+
+ Object getColumnData(int i);
+
+ Object getNextDataToken() throws Exception;
+
+ String getNextToken() throws Exception;
+
+ void parseDataBlockParameters(String[] fields, String key, String data, int[] key2col, int[] col2key) throws Exception;
+
+ String readLine();
+
+ GenericCifDataParser set(GenericLineReader reader, BufferedReader br, boolean debugging);
+
+ String toUnicode(String data);
+
+ String skipLoop(boolean doReport) throws Exception;
+
+ String fixKey(String key);
+
+}
--- /dev/null
+package javajs.api;
+
+/**
+ * GenericColor allows both java.awt.Color and javajs.awt.Color to be
+ * handled by methods that need not distinguish between them. It is used
+ * in the javajs package for the background color of a javajs.swing.JComponent
+ *
+ * @author hansonr
+ *
+ */
+public interface GenericColor {
+
+ int getRGB();
+
+ int getOpacity255();
+
+ void setOpacity255(int a);
+
+}
--- /dev/null
+package javajs.api;
+
+public interface GenericImageDialog {
+
+ void closeMe();
+
+ void setImage(Object image);
+
+}
--- /dev/null
+package javajs.api;
+
+import java.util.Map;
+
+import javajs.util.OC;
+
+public interface GenericImageEncoder {
+
+ public boolean createImage(String type, OC out,
+ Map<String, Object> params) throws Exception;
+
+}
--- /dev/null
+package javajs.api;
+
+public interface GenericLineReader {
+ public String readNextLine() throws Exception;
+}
--- /dev/null
+package javajs.api;
+
+public interface GenericOutputChannel {
+
+ boolean isBigEndian();
+
+ void writeByteAsInt(int b);
+
+ void write(byte[] b, int off, int n);
+
+ void writeInt(int i);
+
+ void reset();
+
+ String closeChannel();
+
+ void writeLong(long b);
+
+ void writeShort(short i);
+
+
+}
--- /dev/null
+package javajs.api;
+
+
+import java.io.InputStream;
+import java.util.zip.ZipInputStream;
+
+public class GenericZipInputStream extends ZipInputStream implements ZInputStream {
+
+ public GenericZipInputStream(InputStream in) {
+ super(in);
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package javajs.api;
+
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import java.util.Map;
+
+
+public interface GenericZipTools {
+
+ public ZInputStream newZipInputStream(InputStream is);
+
+ public String getZipDirectoryAsStringAndClose(BufferedInputStream t);
+
+ public InputStream newGZIPInputStream(InputStream bis) throws IOException;
+
+ public Object getZipFileDirectory(BufferedInputStream bis,
+ String[] subFileList, int listPtr, boolean asBufferedInputStream);
+
+ public String[] getZipDirectoryAndClose(BufferedInputStream t,
+ String manifestID);
+
+ public void getAllZipData(InputStream bis, String[] subFileList,
+ String replace, String binaryFileList, String exclude,
+ Map<String, String> fileData);
+
+ public Object getZipFileContentsAsBytes(BufferedInputStream bis,
+ String[] subFileList, int i);
+
+ public void addZipEntry(Object zos, String fileName) throws IOException;
+
+ public void closeZipEntry(Object zos) throws IOException;
+
+ public Object getZipOutputStream(Object bos);
+
+ public int getCrcValue(byte[] bytes);
+
+ public void readFileAsMap(BufferedInputStream is, Map<String, Object> bdata, String name);
+
+ public String cacheZipContents(BufferedInputStream bis, String shortName,
+ Map<String, Object> cache, boolean asByteArray);
+
+ BufferedInputStream getUnGzippedInputStream(byte[] bytes);
+}
--- /dev/null
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2006 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package javajs.api;
+
+public class Interface {
+
+ public static Object getInterface(String name) {
+ try {
+ Class<?> x = Class.forName(name);
+ return (x == null ? null : x.newInstance());
+ } catch (Exception e) {
+ System.out.println("Interface.getInterface Error creating instance for " + name + ": \n" + e);
+ return null;
+ }
+ }
+
+ public static Object getInstanceWithParams(String name, Class<?>[] classes, Object... params) {
+ try {
+ Class<?> cl = Class.forName(name);
+ return cl.getConstructor(classes).newInstance(params);
+ } catch (Exception e) {
+ System.out.println("Interface.getInterfaceWithParams Error creating instance for " + name + ": \n" + e);
+ return null;
+ }
+ }
+
+
+}
--- /dev/null
+package javajs.api;
+
+/**
+ * A flag that this object is really a JavaScript function that, for example,
+ * might be called from setTimeout().
+ *
+ * @author Bob Hanson
+ *
+ */
+public interface JSFunction {
+
+}
--- /dev/null
+package javajs.api;
+
+/**
+ * called by JSmol JavaScript methods using
+ *
+ * this._applet.xxxx()
+ *
+ */
+public interface JSInterface {
+
+ int cacheFileByName(String fileName, boolean isAdd);
+ void cachePut(String key, Object data);
+ void destroy();
+ String getFullName();
+ void openFileAsyncSpecial(String fileName, int flags);
+ boolean processMouseEvent(int id, int x, int y, int modifiers, long time);
+ void processTwoPointGesture(float[][][] touches);
+ void setDisplay(Object canvas);
+ void setScreenDimension(int width, int height);
+ boolean setStatusDragDropped(int mode, int x, int y, String fileName);
+ void startHoverWatcher(boolean enable);
+
+ // these are not general methods
+//Object getGLmolView();
+//String loadInlineString(String mol, String script, boolean isAppend);
+//String openFile(String fileName);
+
+}
+
--- /dev/null
+package javajs.api;
+
+public interface JSONEncodable {
+
+ String toJSON();
+
+}
--- /dev/null
+package javajs.api;
+
+public interface ResettableStream {
+
+ void resetStream();
+
+}
--- /dev/null
+package javajs.api;
+
+public interface ZInputStream {
+ // placeholder for ZipInputStream not requiring direct access to java.util.zip
+
+}
--- /dev/null
+package javajs.api.js;
+
+/**
+ * methods in JSmol JavaScript accessed in Jmol (aka J2S)
+ */
+public interface J2SObjectInterface {
+
+ Object _doAjax(Object url, String postOut, Object bytesOrStringOut, boolean isBinary);
+
+ void _apply(Object func, Object data);
+
+}
--- /dev/null
+package javajs.api.js;
+
+/**
+ * called by JSmol JavaScript methods using
+ *
+ * this._applet.xxxx()
+ *
+ */
+public interface JSInterface {
+
+ int cacheFileByName(String fileName, boolean isAdd);
+
+ void cachePut(String key, Object data);
+
+ void destroy();
+
+ String getFullName();
+
+ void openFileAsyncSpecial(String fileName, int flags);
+
+ boolean processMouseEvent(int id, int x, int y, int modifiers, long time);
+
+ void processTwoPointGesture(float[][][] touches);
+
+ void setDisplay(Object canvas);
+
+ void setScreenDimension(int width, int height);
+
+ boolean setStatusDragDropped(int mode, int x, int y, String fileName);
+
+ void startHoverWatcher(boolean enable);
+
+
+
+ // these are not general methods
+ // Object getGLmolView();
+ // String loadInlineString(String mol, String script, boolean isAppend);
+ // String openFile(String fileName);
+
+}
+
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2009-06-30 18:58:33 -0500 (Tue, 30 Jun 2009) $
+ * $Revision: 11158 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2002-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.export;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javajs.util.Lst;
+import javajs.util.SB;
+
+
+
+public class PDFCreator {
+
+ private OutputStream os;
+ private Lst<PDFObject> indirectObjects;
+ private PDFObject root;
+ private PDFObject graphics;
+// private PDFObject pageResources;
+// private PDFObject graphicsResources;
+
+ private int pt;
+ private int xrefPt;
+ private int count;
+
+ private int height;
+ private int width;
+
+ private Map<String, PDFObject>fonts;
+
+ public PDFCreator() {
+ // for Class.forName
+ }
+
+ public void setOutputStream(OutputStream os) {
+ this.os = os;
+ }
+
+ public void newDocument(int paperWidth, int paperHeight, boolean isLandscape) {
+ width = (isLandscape ? paperHeight : paperWidth);
+ height = (isLandscape ? paperWidth : paperHeight);
+ System.out.println("Creating PDF with width=" + width + " and height=" + height);
+ fonts = new Hashtable<String, PDFObject>();
+ indirectObjects = new Lst<PDFObject>();
+ //graphicsResources = newObject(null);
+ //pageResources = newObject(null); // will set this to compressed stream later
+ root = newObject("Catalog");
+ PDFObject pages = newObject("Pages");
+ PDFObject page = newObject("Page");
+ PDFObject pageContents = newObject(null);
+ graphics = newObject("XObject");
+
+ root.addDef("Pages", pages.getRef());
+ pages.addDef("Count", "1");
+ pages.addDef("Kids", "[ " + page.getRef() +" ]");
+ page.addDef("Parent", pages.getRef());
+ page.addDef("MediaBox", "[ 0 0 " + paperWidth + " " + paperHeight + " ]");
+ if (isLandscape)
+ page.addDef("Rotate", "90");
+
+ pageContents.addDef("Length", "?");
+ pageContents.append((isLandscape ? "q 0 1 1 0 0 0 " : "q 1 0 0 -1 0 "+(paperHeight))+" cm /" + graphics.getID() + " Do Q");
+ page.addDef("Contents", pageContents.getRef());
+ addProcSet(page);
+ addProcSet(graphics);
+ // will add fonts as well as they are needed
+ graphics.addDef("Subtype", "/Form");
+ graphics.addDef("FormType", "1");
+ graphics.addDef("BBox", "[0 0 " + width + " " + height + "]");
+ graphics.addDef("Matrix", "[1 0 0 1 0 0]");
+ graphics.addDef("Length", "?");
+ page.addResource("XObject", graphics.getID(), graphics.getRef());
+ g("q 1 w 1 J 1 j 10 M []0 d q "); // line width 1, line cap circle, line join circle, miter limit 10, solid
+ clip(0, 0, width, height);
+ }
+
+ private void addProcSet(PDFObject o) {
+ o.addResource(null, "ProcSet", "[/PDF /Text /ImageB /ImageC /ImageI]");
+ }
+
+ private void clip(int x1, int y1, int x2, int y2) {
+ moveto(x1, y1);
+ lineto(x2, y1);
+ lineto(x2, y2);
+ lineto(x1, y2);
+ g("h W n");
+ }
+
+ public void moveto(int x, int y) {
+ g(x + " " + y + " m");
+ }
+
+ public void lineto(int x, int y) {
+ g(x + " " + y + " l");
+ }
+
+ private PDFObject newObject(String type) {
+ PDFObject o = new PDFObject(++count);
+ if (type != null)
+ o.addDef("Type", "/" + type);
+ indirectObjects.addLast(o);
+ return o;
+ }
+
+ public void addInfo(Map<String, String> data) {
+ Hashtable<String, Object> info = new Hashtable<String, Object>();
+ for (Entry<String, String> e: data.entrySet()) {
+ String value = "(" + e.getValue().replace(')','_').replace('(','_')+ ")";
+ info.put(e.getKey(), value);
+ }
+ root.addDef("Info", info);
+ }
+
+ private PDFObject addFontResource(String fname) {
+ PDFObject f = newObject("Font");
+ fonts.put(fname, f);
+ f.addDef("BaseFont", fname);
+ f.addDef("Encoding", "/WinAnsiEncoding");
+ f.addDef("Subtype", "/Type1");
+ graphics.addResource("Font", f.getID(), f.getRef());
+ return f;
+ }
+
+ private Map<Object, PDFObject> images;
+
+ public void addImageResource(Object newImage, int width, int height, int[] buffer, boolean isRGB) {
+ PDFObject imageObj = newObject("XObject");
+ if (images == null)
+ images = new Hashtable<Object, PDFObject>();
+ images.put(newImage, imageObj);
+ imageObj.addDef("Subtype", "/Image");
+ imageObj.addDef("Length", "?");
+ imageObj.addDef("ColorSpace", isRGB ? "/DeviceRGB" : "/DeviceGray");
+ imageObj.addDef("BitsPerComponent", "8");
+ imageObj.addDef("Width", "" + width);
+ imageObj.addDef("Height", "" + height);
+ graphics.addResource("XObject", imageObj.getID(), imageObj.getRef());
+ int n = buffer.length;
+ byte[] stream = new byte[n * (isRGB ? 3 : 1)];
+ if (isRGB) {
+ for (int i = 0, pt = 0; i < n; i++) {
+ stream[pt++] = (byte) ((buffer[i] >> 16) & 0xFF);
+ stream[pt++] = (byte) ((buffer[i] >> 8) & 0xFF);
+ stream[pt++] = (byte) (buffer[i] & 0xFF);
+ }
+ } else {
+ for (int i = 0; i < n; i++)
+ stream[i] = (byte) buffer[i];
+ }
+ imageObj.setStream(stream);
+ graphics.addResource("XObject", imageObj.getID(), imageObj.getRef());
+ }
+
+ public void g(String cmd) {
+ graphics.append(cmd).appendC('\n');
+ }
+
+ private void output(String s) throws IOException {
+ byte[] b = s.getBytes();
+ os.write(b, 0, b.length);
+ pt += b.length;
+ }
+
+ public void closeDocument() throws IOException {
+ g("Q Q");
+ outputHeader();
+ writeObjects();
+ writeXRefTable();
+ writeTrailer();
+ os.flush();
+ os.close();
+ }
+
+ private void outputHeader() throws IOException {
+ output("%PDF-1.3\n%");
+ byte[] b = new byte[] {-1, -1, -1, -1};
+ os.write(b, 0, b.length);
+ pt += 4;
+ output("\n");
+ }
+
+ private void writeTrailer() throws IOException {
+ PDFObject trailer = new PDFObject(-2);
+ output("trailer");
+ trailer.addDef("Size", "" + indirectObjects.size());
+ trailer.addDef("Root", root.getRef());
+ trailer.output(os);
+ output("startxref\n");
+ output("" + xrefPt + "\n");
+ output("%%EOF\n");
+ }
+
+ /**
+ * Write Font objects first.
+ *
+ * @throws IOException
+ */
+ private void writeObjects() throws IOException {
+ int nObj = indirectObjects.size();
+ for (int i = 0; i < nObj; i++) {
+ PDFObject o = indirectObjects.get(i);
+ if (!o.isFont())
+ continue;
+ o.pt = pt;
+ pt += o.output(os);
+ }
+ for (int i = 0; i < nObj; i++) {
+ PDFObject o = indirectObjects.get(i);
+ if (o.isFont())
+ continue;
+ o.pt = pt;
+ pt += o.output(os);
+ }
+ }
+
+ private void writeXRefTable() throws IOException {
+ xrefPt = pt;
+ int nObj = indirectObjects.size();
+ SB sb = new SB();
+ // note trailing space, needed because \n is just one character
+ sb.append("xref\n0 " + (nObj + 1)
+ + "\n0000000000 65535 f\r\n");
+ for (int i = 0; i < nObj; i++) {
+ PDFObject o = indirectObjects.get(i);
+ String s = "0000000000" + o.pt;
+ sb.append(s.substring(s.length() - 10));
+ sb.append(" 00000 n\r\n");
+ }
+ output(sb.toString());
+ }
+
+ public boolean canDoLineTo() {
+ return true;
+ }
+
+ public void fill() {
+ g("f");
+ }
+
+ public void stroke() {
+ g("S");
+ }
+
+ public void doCircle(int x, int y, int r, boolean doFill) {
+ double d = r*4*(Math.sqrt(2)-1)/3;
+ double dx = x;
+ double dy = y;
+ g((dx + r) + " " + dy + " m");
+ g((dx + r) + " " + (dy + d) + " " + (dx + d) + " " + (dy + r) + " " + (dx) + " " + (dy + r) + " " + " c");
+ g((dx - d) + " " + (dy + r) + " " + (dx - r) + " " + (dy + d) + " " + (dx - r) + " " + (dy) + " c");
+ g((dx - r) + " " + (dy - d) + " " + (dx - d) + " " + (dy - r) + " " + (dx) + " " + (dy - r) + " c");
+ g((dx + d) + " " + (dy - r) + " " + (dx + r) + " " + (dy - d) + " " + (dx + r) + " " + (dy) + " c");
+ g(doFill ? "f" : "s");
+ }
+
+ public void doPolygon(int[] axPoints, int[] ayPoints, int nPoints, boolean doFill) {
+ moveto(axPoints[0], ayPoints[0]);
+ for (int i = 1; i < nPoints; i++)
+ lineto(axPoints[i], ayPoints[i]);
+ g(doFill ? "f" : "s");
+ }
+
+ public void doRect(int x, int y, int width, int height, boolean doFill) {
+ g(x + " " + y + " " + width + " " + height + " re " + (doFill ? "f" : "s"));
+ }
+
+ public void drawImage(Object image, int destX0, int destY0,
+ int destX1, int destY1, int srcX0, int srcY0, int srcX1, int srcY1) {
+ PDFObject imageObj = images.get(image);
+ if (imageObj == null)
+ return;
+ g("q");
+ clip(destX0, destY0, destX1, destY1);
+ double iw = Double.parseDouble((String) imageObj.getDef("Width"));
+ double ih = Double.parseDouble((String) imageObj.getDef("Height"));
+ double dw = (destX1 - destX0 + 1);
+ double dh = (destY1 - destY0 + 1);
+ double sw = (srcX1 - srcX0 + 1);
+ double sh = (srcY1 - srcY0 + 1);
+ double scaleX = dw / sw;
+ double scaleY = dh / sh;
+ double transX = destX0 - srcX0 * scaleX;
+ double transY = destY0 + (ih - srcY0) * scaleY;
+ g(scaleX*iw + " 0 0 " + -scaleY*ih + " " + transX + " " + transY + " cm");
+ g("/" + imageObj.getID() + " Do");
+ g("Q");
+ }
+
+ public void drawStringRotated(String s, int x, int y, int angle) {
+ g("q " + getRotation(angle) + " " + x + " " + y
+ + " cm BT(" + s + ")Tj ET Q");
+ }
+
+ public String getRotation(int angle) {
+ float cos = 0, sin = 0;
+ switch (angle) {
+ case 0:
+ cos = 1;
+ break;
+ case 90:
+ sin = 1;
+ break;
+ case -90:
+ sin = -1;
+ break;
+ case 180:
+ cos = -1;
+ break;
+ default:
+ float a = (float) (angle * (Math.PI / 180));
+ cos = (float) Math.cos(a);
+ sin = (float) Math.sin(a);
+ if (Math.abs(cos) < 0.0001)
+ cos = 0;
+ if (Math.abs(sin) < 0.0001)
+ sin = 0;
+ }
+ return cos + " " + sin + " " + sin + " " + -cos;
+ }
+
+ public void setColor(float[] rgb, boolean isFill) {
+ g(rgb[0] + " " + rgb[1] + " " + rgb[2] + (isFill ? " rg" : " RG"));
+ }
+
+ public void setFont(String fname, float size) {
+ PDFObject f = fonts.get(fname);
+ if (f == null)
+ f = addFontResource(fname);
+ g("/" + f.getID() + " " + size + " Tf");
+ }
+
+ public void setLineWidth(float width) {
+ g(width + " w");
+ }
+
+ public void translateScale(float x, float y, float scale) {
+ g(scale + " 0 0 " + scale + " " + x + " " + y + " cm");
+ }
+
+}
--- /dev/null
+package javajs.export;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.zip.Deflater;
+import java.util.zip.DeflaterOutputStream;
+
+import javajs.util.SB;
+
+
+/**
+ * A rudimentary class for working with PDF document creation.
+ * Written from scratch based on PDF Reference 13.
+ *
+ * @author hansonr Bob Hanson hansonr@stolaf.edu 10/28/2013
+ *
+ */
+class PDFObject extends SB {
+ private Map<String, Object> dictionary;
+ private byte[] stream;
+ private int index;
+ String type;
+ int len;
+ int pt;
+
+ PDFObject(int index) {
+ this.index = index;
+ }
+
+ String getRef() {
+ return index + " 0 R";
+ }
+
+ String getID() {
+ return type.substring(0, 1) + index;
+ }
+
+ boolean isFont() {
+ return "Font".equals(type);
+ }
+
+ void setStream(byte[] stream) {
+ this.stream = stream;
+ }
+
+ Object getDef(String key) {
+ return dictionary.get(key);
+ }
+
+ void addDef(String key, Object value) {
+ if (dictionary == null)
+ dictionary = new Hashtable<String, Object>();
+ dictionary.put(key, value);
+ if (key.equals("Type"))
+ type = ((String) value).substring(1);
+ }
+
+ void setAsStream() {
+ stream = toBytes(0, -1);
+ setLength(0);
+ }
+
+ int output(OutputStream os) throws IOException {
+ if (index > 0) {
+ String s = index + " 0 obj\n";
+ write(os, s.getBytes(), 0);
+ }
+ int streamLen = 0;
+ if (dictionary != null) {
+ if (dictionary.containsKey("Length")) {
+ if (stream == null)
+ setAsStream();
+ streamLen = stream.length;
+ boolean doDeflate = (streamLen > 1000);
+ if (doDeflate) {
+ Deflater deflater = new Deflater(9);
+ ByteArrayOutputStream outBytes = new ByteArrayOutputStream(1024);
+ DeflaterOutputStream compBytes = new DeflaterOutputStream(outBytes,
+ deflater);
+ compBytes.write(stream, 0, streamLen);
+ compBytes.finish();
+ stream = outBytes.toByteArray();
+ dictionary.put("Filter", "/FlateDecode");
+ streamLen = stream.length;
+ }
+ dictionary.put("Length", "" + streamLen);
+ }
+ write(os, getDictionaryText(dictionary, "\n").getBytes(), 0);
+ }
+ if (length() > 0)
+ write(os, this.toString().getBytes(), 0);
+ if (stream != null) {
+ write(os, "stream\r\n".getBytes(), 0);
+ write(os, stream, streamLen);
+ write(os, "\r\nendstream\r\n".getBytes(), 0);
+ }
+ if (index > 0)
+ write(os, "endobj\n".getBytes(), 0);
+ return len;
+ }
+
+ private void write(OutputStream os, byte[] bytes, int nBytes) throws IOException {
+ if (nBytes == 0)
+ nBytes = bytes.length;
+ len += nBytes;
+ os.write(bytes, 0, nBytes);
+ }
+
+ @SuppressWarnings("unchecked")
+ private String getDictionaryText(Map<String, Object> d, String nl) {
+ SB sb = new SB();
+ sb.append("<<");
+ if (d.containsKey("Type"))
+ sb.append("/Type").appendO(d.get("Type"));
+ for (Entry<String, Object> e : d.entrySet()) {
+ String s = e.getKey();
+ if (s.equals("Type") || s.startsWith("!"))
+ continue;
+ sb.append("/" + s);
+ Object o = e.getValue();
+ if (o instanceof Map<?, ?>) {
+ sb.append((getDictionaryText((Map<String, Object>) o, "")));
+ continue;
+ }
+ s = (String) e.getValue();
+ if (!s.startsWith("/"))
+ sb.append(" ");
+ sb.appendO(s);
+ }
+ return (sb.length() > 3 ? sb.append(">>").append(nl).toString() : "");
+ }
+
+ @SuppressWarnings("unchecked")
+ private Map<String, Object> createSubdict(Map<String, Object> d0, String dict) {
+ Map<String, Object> d = (Map<String, Object>) d0.get(dict);
+ if (d == null)
+ d0.put(dict, d = new Hashtable<String, Object>());
+ return d;
+ }
+
+ void addResource(String type, String key, String value) {
+ Map<String, Object> r = createSubdict(dictionary, "Resources");
+ if (type != null)
+ r = createSubdict(r, type);
+ r.put(key, value);
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: nicove $
+ * $Date: 2007-03-30 12:26:16 -0500 (Fri, 30 Mar 2007) $
+ * $Revision: 7275 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2002-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.img;
+
+import java.io.BufferedInputStream;
+import java.io.IOException;
+
+import javajs.util.Rdr;
+
+/**
+ * src: http://www.javaworld.com/article/2077542/learn-java/java-tip-43--how-to-
+ * read-8--and-24-bit-microsoft-windows-bitmaps-in-java-applications.html
+ *
+ * see also: http://en.wikipedia.org/wiki/BMP_file_format
+ *
+ * Modified by Bob Hanson hansonr@stolaf.edu
+ *
+ * @author Bob Hanson (hansonr@stolaf.edu)
+ *
+ */
+public class BMPDecoder {
+
+ public BMPDecoder() {
+ // for reflection
+ }
+
+ private BufferedInputStream bis;
+
+ /**
+ * original comment:
+ *
+ * loadbitmap() method converted from Windows C code. Reads only uncompressed
+ * 24- and 8-bit images. Tested with images saved using Microsoft Paint in
+ * Windows 95. If the image is not a 24- or 8-bit image, the program refuses
+ * to even try. I guess one could include 4-bit images by masking the byte by
+ * first 1100 and then 0011. I am not really interested in such images. If a
+ * compressed image is attempted, the routine will probably fail by generating
+ * an IOException. Look for variable ncompression to be different from 0 to
+ * indicate compression is present.
+ *
+ * @param bytes
+ * @return [image byte array, width, height]
+ */
+ public Object[] decodeWindowsBMP(byte[] bytes) {
+ try {
+ bis = Rdr.getBIS(bytes);
+ temp = new byte[4];
+ // read BITMAPFILEHEADER
+ if (readByte() != 'B' || readByte() != 'M')
+ return null;
+ readInt(); // file size; ignored
+ readShort(); // reserved
+ readShort(); // reserved
+ readInt(); // ptr to pixel array; ignored
+ int imageWidth, imageHeight, bitsPerPixel, nColors = 0, imageSize = 0;
+ // read BITMAP header
+ int headerSize = readInt();
+ switch (headerSize) {
+ case 12:
+ // BITMAPCOREHEADER
+ imageWidth = readShort();
+ imageHeight = readShort();
+ readShort(); // planes
+ bitsPerPixel = readShort();
+ break;
+ case 40:
+ // BITMAPINFOHEADER
+ imageWidth = readInt();
+ imageHeight = readInt();
+ readShort(); // planes
+ bitsPerPixel = readShort();
+ int ncompression = readInt();
+ if (ncompression != 0) {
+ System.out.println("BMP Compression is :" + ncompression
+ + " -- aborting");
+ return null;
+ }
+ imageSize = readInt();
+ readInt(); // hres
+ readInt(); // vres
+ nColors = readInt();
+ readInt(); // colors used
+ break;
+ default:
+ System.out.println("BMP Header unrecognized, length=" + headerSize
+ + " -- aborting");
+ return null;
+ }
+ boolean isYReversed = (imageHeight < 0);
+ if (isYReversed)
+ imageHeight = -imageHeight;
+ int nPixels = imageHeight * imageWidth;
+ int bytesPerPixel = bitsPerPixel / 8;
+ nColors = (nColors > 0 ? nColors : 1 << bitsPerPixel);
+ int npad = (bytesPerPixel == 4 ? 0
+ : imageSize == 0 ? 4 - (imageWidth % 4) : (imageSize / imageHeight)
+ - imageWidth * bytesPerPixel) % 4;
+ int[] palette;
+ int[] buf = new int[nPixels];
+ int dpt = (isYReversed ? imageWidth : -imageWidth);
+ int pt0 = (isYReversed ? 0 : nPixels + dpt);
+ int pt1 = (isYReversed ? nPixels : dpt);
+ switch (bitsPerPixel) {
+ case 32:
+ case 24:
+ for (int pt = pt0; pt != pt1; pt += dpt, pad(npad))
+ for (int i = 0; i < imageWidth; i++)
+ buf[pt + i] = readColor(bytesPerPixel);
+ break;
+ case 8:
+ palette = new int[nColors];
+ for (int i = 0; i < nColors; i++)
+ palette[i] = readColor(4);
+ for (int pt = pt0; pt != pt1; pt += dpt, pad(npad))
+ for (int i = 0; i < imageWidth; i++)
+ buf[pt + i] = palette[readByte()];
+ break;
+ case 4:
+ npad = (4 - (((imageWidth + 1) / 2) % 4)) % 4;
+ palette = new int[nColors];
+ for (int i = 0; i < nColors; i++)
+ palette[i] = readColor(4);
+ int b4 = 0;
+ for (int pt = pt0; pt != pt1; pt += dpt, pad(npad))
+ for (int i = 0, shift = 4; i < imageWidth; i++, shift = 4 - shift)
+ buf[pt + i] = palette[((shift == 4 ? (b4 = readByte()) : b4) >> shift) & 0xF];
+ break;
+ case 1:
+ int color1 = readColor(3);
+ int color2 = readColor(3);
+ npad = (4 - (((imageWidth + 7) / 8) % 4)) % 4;
+ int b = 0;
+ for (int pt = pt0; pt != pt1; pt += dpt, pad(npad))
+ for (int i = 0, bpt = -1; i < imageWidth; i++, bpt--) {
+ if (bpt < 0) {
+ b = readByte();
+ bpt = 7;
+ }
+ buf[pt + i] = ((b & (1 << bpt)) == 0 ? color1 : color2);
+ }
+ break;
+ case 64:
+ case 2:
+ default:
+ System.out
+ .println("Not a 32-, 24-, 8-, 4-, or 1-bit Windows Bitmap, aborting...");
+ return null;
+ }
+ return new Object[] { buf, Integer.valueOf(imageWidth),
+ Integer.valueOf(imageHeight) };
+ } catch (Exception e) {
+ System.out.println("Caught exception in loadbitmap!");
+ }
+ return null;
+ }
+
+ private boolean pad(int npad) throws IOException {
+ for (int i = 0; i < npad; i++)
+ readByte();
+ return true;
+ }
+
+ private byte[] temp;
+
+ private int readColor(int n) throws IOException {
+ bis.read(temp, 0, n);
+ return 0xff << 24 | ((temp[2] & 0xff) << 16)
+ | ((temp[1] & 0xff) << 8) | temp[0] & 0xff;
+ }
+
+ private int readInt() throws IOException {
+ bis.read(temp, 0, 4);
+ return ((temp[3] & 0xff) << 24) | ((temp[2] & 0xff) << 16)
+ | ((temp[1] & 0xff) << 8) | temp[0] & 0xff;
+ }
+
+ private int readShort() throws IOException {
+ bis.read(temp, 0, 2);
+ return ((temp[1] & 0xff) << 8) | temp[0] & 0xff;
+ }
+
+ private int readByte() throws IOException {
+ bis.read(temp, 0, 1);
+ return temp[0] & 0xff;
+ }
+
+}
--- /dev/null
+package javajs.img;
+
+import java.util.zip.CRC32;
+
+
+import javajs.util.AU;
+
+abstract class CRCEncoder extends ImageEncoder {
+
+ protected int startPos, bytePos;
+
+ private CRC32 crc;
+ protected byte[] pngBytes;
+ protected int dataLen;
+ private byte[] int2 = new byte[2];
+ private byte[] int4 = new byte[4];
+
+ CRCEncoder() {
+ pngBytes = new byte[250];
+ crc = new CRC32();
+ }
+
+ protected void setData(byte[] b, int pt) {
+ pngBytes = b;
+ dataLen = b.length;
+ startPos = bytePos = pt;
+ }
+
+ protected byte[] getBytes() {
+ return (dataLen == pngBytes.length ? pngBytes : AU.arrayCopyByte(
+ pngBytes, dataLen));
+ }
+
+ protected void writeCRC() {
+ crc.reset();
+ crc.update(pngBytes, startPos, bytePos - startPos);
+ writeInt4((int) crc.getValue());
+ }
+
+ /**
+ * Write a two-byte integer into the pngBytes array at a given position.
+ *
+ * @param n The integer to be written into pngBytes.
+ */
+ protected void writeInt2(int n) {
+ int2[0] = (byte) ((n >> 8) & 0xff);
+ int2[1] = (byte) (n & 0xff);
+ writeBytes(int2);
+ }
+
+ /**
+ * Write a four-byte integer into the pngBytes array at a given position.
+ *
+ * @param n The integer to be written into pngBytes.
+ */
+ protected void writeInt4(int n) {
+ getInt4(n, int4);
+ writeBytes(int4);
+ }
+
+ protected static void getInt4(int n, byte[] int4) {
+ int4[0] = (byte) ((n >> 24) & 0xff);
+ int4[1] = (byte) ((n >> 16) & 0xff);
+ int4[2] = (byte) ((n >> 8) & 0xff);
+ int4[3] = (byte) (n & 0xff);
+ }
+
+ /**
+ * Write a single byte into the pngBytes array at a given position.
+ *
+ * @param b The byte to be written into pngBytes.
+ */
+ protected void writeByte(int b) {
+ byte[] temp = {
+ (byte) b
+ };
+ writeBytes(temp);
+ }
+
+ /**
+ * Write a string into the pngBytes array at a given position.
+ * This uses the getBytes method, so the encoding used will
+ * be its default.
+ *
+ * @param s The string to be written into pngBytes.
+ * @see java.lang.String#getBytes()
+ */
+ protected void writeString(String s) {
+ writeBytes(s.getBytes());
+ }
+
+ /**
+ * Write an array of bytes into the pngBytes array.
+ * Both dataLen and bytePos are updated. If we don't have
+ * enough room, this is certainly in image data writing,
+ * so we add just enough for CRC END CRC
+ *
+ * @param data
+ * The data to be written into pngBytes.
+ */
+ protected void writeBytes(byte[] data) {
+ int newPos = bytePos + data.length;
+ dataLen = Math.max(dataLen, newPos);
+ if (newPos > pngBytes.length)
+ pngBytes = AU.arrayCopyByte(pngBytes, newPos + 16);
+ System.arraycopy(data, 0, pngBytes, bytePos, data.length);
+ bytePos = newPos;
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-06-02 12:14:13 -0500 (Sat, 02 Jun 2007) $
+ * $Revision: 7831 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2000-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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.
+ */
+
+// Final encoding code from http://acme.com/resources/classes/Acme/JPM/Encoders/GifEncoder.java
+//
+// GifEncoder - write out an image as a GIF
+//
+//
+// Transparency handling and variable bit size courtesy of Jack Palevich.
+//
+// Copyright (C)1996,1998 by Jef Poskanzer <jef@mail.acme.com>. All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+// OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+// HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+//
+// Visit the ACME Labs Java page for up-to-date versions of this and other
+// fine Java utilities: http://www.acme.com/java/
+//
+/// Write out an image as a GIF.
+// <P>
+// <A HREF="/resources/classes/Acme/JPM/Encoders/GifEncoder.java">Fetch the software.</A><BR>
+// <A HREF="/resources/classes/Acme.tar.gz">Fetch the entire Acme package.</A>
+// <P>
+// @see ToGif
+
+package javajs.img;
+
+import javajs.util.CU;
+import javajs.util.Lst;
+import javajs.util.M3;
+import javajs.util.P3;
+
+import java.util.Hashtable;
+import java.util.Map;
+import java.io.IOException;
+
+/**
+ *
+ * GifEncoder extensively adapted for Jmol by Bob Hanson
+ *
+ * Color quantization roughly follows the GIMP method
+ * "dither Floyd-Steinberg (normal)" but with some twists. (For example, we
+ * exclude the background color.)
+ *
+ * Note that although GIMP code annotation refers to "median-cut", it is really
+ * using MEAN-cut. That is what I use here as well.
+ *
+ * -- commented code allows visualization of the color space using Jmol. Very
+ * enlightening!
+ *
+ * -- much simplified interface with ImageEncoder
+ *
+ * -- uses simple Hashtable with Integer() to catalog colors
+ *
+ * -- allows progressive production of animated GIF via Jmol CAPTURE command
+ *
+ * -- uses general purpose javajs.util.OutputChannel for byte-handling options
+ * such as posting to a server, writing to disk, and retrieving bytes.
+ *
+ * -- allows JavaScript port
+ *
+ * -- Bob Hanson, first try: 24 Sep 2013; final coding: 9 Nov 2014
+ *
+ *
+ * @author Bob Hanson hansonr@stolaf.edu
+ */
+
+public class GifEncoder extends ImageEncoder {
+
+ private Map<String, Object> params;
+ private P3[] palette;
+ private int backgroundColor;
+
+ private boolean interlaced;
+ private boolean addHeader = true;
+ private boolean addImage = true;
+ private boolean addTrailer = true;
+ private boolean isTransparent;
+ private boolean floydSteinberg = true;
+ private boolean capturing;
+ private boolean looping;
+
+ private int delayTime100ths = -1;
+ private int bitsPerPixel = 1;
+
+ private int byteCount;
+
+ /**
+ * we allow for animated GIF by being able to re-enter the code with different
+ * parameters held in params
+ *
+ *
+ */
+ @Override
+ protected void setParams(Map<String, Object> params) {
+ this.params = params;
+ Integer ic = (Integer) params.get("transparentColor");
+ if (ic == null) {
+ ic = (Integer) params.get("backgroundColor");
+ if (ic != null)
+ backgroundColor = ic.intValue();
+ } else {
+ backgroundColor = ic.intValue();
+ isTransparent = true;
+ }
+
+ interlaced = (Boolean.TRUE == params.get("interlaced"));
+ if (params.containsKey("captureRootExt") // file0000.gif
+ || !params.containsKey("captureMode")) // animated gif
+ return;
+ interlaced = false;
+ capturing = true;
+ try {
+ byteCount = ((Integer) params.get("captureByteCount")).intValue();
+ } catch (Exception e) {
+ // ignore
+ }
+ switch ("maec"
+ .indexOf(((String) params.get("captureMode")).substring(0, 1))) {
+ case 0: //"movie"
+ params.put("captureMode", "add");
+ addImage = false;
+ addTrailer = false;
+ break;
+ case 1: // add
+ addHeader = false;
+ addTrailer = false;
+ int fps = Math.abs(((Integer) params.get("captureFps")).intValue());
+ delayTime100ths = (fps == 0 ? 0 : 100 / fps);
+ looping = (Boolean.FALSE != params.get("captureLooping"));
+ break;
+ case 2: // end
+ addHeader = false;
+ addImage = false;
+ break;
+ case 3: // cancel
+ addHeader = false;
+ addImage = false;
+ out.cancel();
+ break;
+ }
+ }
+
+ @Override
+ protected void generate() throws IOException {
+ if (addHeader)
+ writeHeader();
+ addHeader = false; // only one header
+ if (addImage) {
+ createPalette();
+ writeGraphicControlExtension();
+ if (delayTime100ths >= 0 && looping)
+ writeNetscapeLoopExtension();
+ writeImage();
+ }
+ }
+
+ @Override
+ protected void close() {
+ if (addTrailer) {
+ writeTrailer();
+ } else {
+ doClose = false;
+ }
+ if (capturing)
+ params.put("captureByteCount", Integer.valueOf(byteCount));
+ }
+
+ ////////////// 256-color quantization //////////////
+
+ /**
+ * a color point in normalized L*a*b space with a flag indicating whether it
+ * is the background color
+ */
+ private class ColorItem extends P3 {
+ /**
+ *
+ */
+ protected boolean isBackground;
+
+ ColorItem(int rgb, boolean isBackground) {
+ this.isBackground = isBackground;
+ setT(toLABnorm(rgb));
+ }
+ }
+
+ /**
+ * A list of normalized L*a*b points with an index and a center and volume
+ *
+ */
+ private class ColorCell extends Lst<P3> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ protected int index;
+ protected P3 center;
+
+ private float volume;
+
+ ColorCell(int index) {
+ this.index = index;
+ }
+
+ /**
+ * @param doVisualize
+ * debugging only
+ * @return volume in normalized L*a*b space
+ */
+ public float getVolume(boolean doVisualize) {
+ if (volume != 0)
+ return volume;
+ if (size() < 2)
+ return -1;
+ //if (true)
+ //return lst.size();
+ //float d;
+ float maxx = -Integer.MAX_VALUE;
+ float minx = Integer.MAX_VALUE;
+ float maxy = -Integer.MAX_VALUE;
+ float miny = Integer.MAX_VALUE;
+ float maxz = -Integer.MAX_VALUE;
+ float minz = Integer.MAX_VALUE;
+ int n = size();
+ for (int i = n; --i >= 0;) {
+ P3 xyz = get(i);
+ if (xyz.x < minx)
+ minx = xyz.x;
+ if (xyz.y < miny)
+ miny = xyz.y;
+ if (xyz.z < minz)
+ minz = xyz.z;
+ if (xyz.x > maxx)
+ maxx = xyz.x;
+ if (xyz.y > maxy)
+ maxy = xyz.y;
+ if (xyz.z > maxz)
+ maxz = xyz.z;
+ }
+ float dx = (maxx - minx);
+ float dy = (maxy - miny);
+ float dz = (maxz - minz);
+ // Jmol visualization only
+ // if (doVisualize) {
+ // P3 ptRGB = toRGB(center);
+ // drawPt(index, -size(), ptRGB);
+ // //for (int i = n; --i >= 0;)
+ // //drawPt(index, i, toRGB(get(i)));
+ // P3 pt0 = toRGB(P3.new3(Math.max(minx, 0), Math.max(miny, 0),
+ // Math.max(minz, 0)));
+ // P3 pt1 = toRGB(P3.new3(Math.min(maxx, 100), Math.min(maxy, 100),
+ // Math.min(maxz, 100)));
+ // rgbToXyz(pt0, pt0);
+ // xyzToLab(pt0, pt0);
+ // rgbToXyz(pt1, pt1);
+ // xyzToLab(pt1, pt1);
+ // System.out.println("boundbox corners " + pt0 + " " + pt1);
+ // System.out.println("draw d" + index + " boundbox color " + ptRGB
+ // + " mesh nofill");
+ // }
+ return volume = dx * dx + dy * dy + dz * dz;
+ }
+
+ // // Jmol visualization only
+ // private void drawPt(int index, int i, P3 rgb) {
+ // boolean isMain = (i < 0);
+ // P3 lab = rgbToXyz(rgb, null);
+ // xyzToLab(lab, lab);
+ // System.out.println("draw d" + index + (isMain ? "_" : "_" + i) + " width "
+ // + (isMain ? 1.0 : 0.2) + " " + lab
+ // + " color " + rgb + (isMain ? " '" + -i + "'" : ""));
+ // }
+
+ /**
+ * Set the average normalized L*a*b value for this cell and return its RGB point
+ *
+ * @return RGB point
+ *
+ */
+ protected P3 setColor() {
+ int count = size();
+ center = new P3();
+ for (int i = count; --i >= 0;)
+ center.add(get(i));
+ center.scale(1f / count);
+ // Jmol visualization only
+ //volume = 0;
+ //getVolume(true);
+ return toRGB(center);
+ }
+
+ /**
+ * use median_cut algorithm to split the cell, creating a doubly linked
+ * list.
+ *
+ * Paul Heckbert, MIT thesis COLOR IMAGE QUANTIZATION FOR FRAME BUFFER
+ * DISPLAY https://www.cs.cmu.edu/~ph/ciq_thesis
+ *
+ * except, as in GIMP, we use center (not median) here.
+ *
+ * @param cells
+ * @return true if split
+ */
+ protected boolean splitCell(Lst<ColorCell> cells) {
+ int n = size();
+ if (n < 2)
+ return false;
+ int newIndex = cells.size();
+ ColorCell newCell = new ColorCell(newIndex);
+ cells.addLast(newCell);
+ float[][] ranges = new float[3][3];
+ for (int ic = 0; ic < 3; ic++) {
+ float low = Float.MAX_VALUE;
+ float high = -Float.MAX_VALUE;
+ for (int i = n; --i >= 0;) {
+ P3 lab = get(i);
+ float v = (ic == 0 ? lab.x : ic == 1 ? lab.y : lab.z);
+ if (low > v)
+ low = v;
+ if (high < v)
+ high = v;
+ }
+ ranges[0][ic] = low;
+ ranges[1][ic] = high;
+ ranges[2][ic] = high - low;
+ }
+ float[] r = ranges[2];
+ int mode = (r[0] >= r[1] ? (r[0] >= r[2] ? 0 : 2) : r[1] >= r[2] ? 1 : 2);
+ float val = ranges[0][mode] + ranges[2][mode] / 2;
+ volume = 0; // recalculate volume if needed
+ switch (mode) {
+ case 0:
+ for (int i = n; --i >= 0;)
+ if (get(i).x >= val)
+ newCell.addLast(removeItemAt(i));
+ break;
+ case 1:
+ for (int i = n; --i >= 0;)
+ if (get(i).y >= val)
+ newCell.addLast(removeItemAt(i));
+ break;
+ case 2:
+ for (int i = size(); --i >= 0;)
+ if (get(i).z >= val)
+ newCell.addLast(removeItemAt(i));
+ break;
+ }
+ return true;
+ }
+ }
+
+ /**
+ * Quantize all colors and create the final palette;
+ * replace pixels[] with an array of color indices.
+ *
+ */
+ private void createPalette() {
+
+ // catalog all pixel colors
+
+ Lst<ColorItem> tempColors = new Lst<ColorItem>();
+ Map<Integer, ColorItem> ciHash = new Hashtable<Integer, ColorItem>();
+ for (int i = 0, n = pixels.length; i < n; i++) {
+ int rgb = pixels[i];
+ Integer key = Integer.valueOf(rgb);
+ ColorItem item = ciHash.get(key);
+ if (item == null) {
+ item = new ColorItem(rgb, rgb == backgroundColor);
+ ciHash.put(key, item);
+ tempColors.addLast(item);
+ }
+ }
+ int nColors = tempColors.size();
+ System.out.println("GIF total image colors: " + nColors);
+ ciHash = null;
+
+ // create a set of <= 256 color cells
+
+ Lst<ColorCell> cells = quantizeColors(tempColors);
+ nColors = cells.size();
+ System.out.println("GIF final color count: " + nColors);
+
+ // generate the palette and map each cell's rgb color to itself
+
+ Map<Integer, ColorCell> colorMap = new Hashtable<Integer, ColorCell>();
+ bitsPerPixel = (nColors <= 2 ? 1 : nColors <= 4 ? 2 : nColors <= 16 ? 4 : 8);
+ palette = new P3[1 << bitsPerPixel];
+ for (int i = 0; i < nColors; i++) {
+ ColorCell c = cells.get(i);
+ colorMap.put(
+ Integer.valueOf(CU.colorPtToFFRGB(palette[i] = c.setColor())), c);
+ }
+
+ // index all pixels to a pallete color
+
+ pixels = indexPixels(cells, colorMap);
+ }
+
+ /**
+ * Quantize colors by generating a set of cells in normalized L*a*b space
+ * containing all colors. Start with just two cells -- fixed background color
+ * and all others. Keep splitting cells while there are fewer than 256 and
+ * some with multiple colors in them.
+ *
+ * It is possible that we will end up with fewer than 256 colors.
+ *
+ * @param tempColors
+ * @return final list of colors
+ */
+ private Lst<ColorCell> quantizeColors(Lst<ColorItem> tempColors) {
+ int n = tempColors.size();
+ Lst<ColorCell> cells = new Lst<ColorCell>();
+ ColorCell cc = new ColorCell(0);
+ cc.addLast(new ColorItem(backgroundColor, true));
+ cells.addLast(cc);
+ cc = new ColorCell(1);
+ if (n > 256)
+ cells.addLast(cc);
+ for (int i = 0; i < n; i++) {
+ ColorItem c = tempColors.get(i);
+ if (c.isBackground)
+ continue;
+ cc.addLast(c);
+ if (n <= 256) {
+ cells.addLast(cc);
+ cc = new ColorCell(cells.size());
+ }
+ }
+ tempColors.clear();
+ if (n > 256)
+ while ((n = cells.size()) < 256) {
+ float maxVol = 0;
+ ColorCell maxCell = null;
+ for (int i = n; --i >= 1;) {
+ ColorCell c = cells.get(i);
+ float v = c.getVolume(false);
+ if (v > maxVol) {
+ maxVol = v;
+ maxCell = c;
+ }
+ }
+ if (maxCell == null || !maxCell.splitCell(cells))
+ break;
+ }
+ return cells;
+ }
+
+ /**
+ *
+ * Assign all colors to their closest approximation and return an array of
+ * color indexes.
+ *
+ * Uses Floyd-Steinberg dithering, finding the closest known color and then
+ * spreading out the error over four leading pixels. Limits error to +/- 75
+ * percent in normalized L*a*b space.
+ *
+ * @param cells
+ * quantized color cells
+ * @param colorMap
+ * map of quantized rgb to its cell
+ * @return array of color indexes, one for each pixel
+ *
+ */
+ private int[] indexPixels(Lst<ColorCell> cells,
+ Map<Integer, ColorCell> colorMap) {
+ // We need a strip only width+2 wide to process all the errors.
+ // Errors are added to the next pixel and the next row's pixels
+ // only through p + width + 1:
+ // p +1
+ // +w-1 +w +w+1
+ // so including p as well, we need a total of width + 2 errors.
+ //
+ // as p moves through the pixels, we just use mod to cycle through
+ // this strip.
+ //
+ int w2 = width + 2;
+ P3[] errors = new P3[w2];
+ // We should replace, not overwrite, pixels
+ // as this may be the raw canvas.buf32.
+ int[] newPixels = new int[pixels.length];
+ P3 err = new P3();
+ P3 lab;
+ int rgb;
+ Map<Integer, ColorCell> nearestCell = new Hashtable<Integer, ColorCell>();
+ for (int i = 0, p = 0; i < height; ++i) {
+ boolean notLastRow = (i != height - 1);
+ for (int j = 0; j < width; ++j, p++) {
+ if (pixels[p] == backgroundColor) {
+ // leave as 0
+ continue;
+ }
+ P3 pe = errors[p % w2];
+ if (pe == null || pe.x == Float.MAX_VALUE) {
+ lab = null;
+ rgb = pixels[p];
+ } else {
+ lab = toLABnorm(pixels[p]);
+ err = pe;
+ // important not to round the clamp here -- full floating precision
+ err.x = clamp(err.x, -75, 75);
+ err.y = clamp(err.y, -75, 75);
+ err.z = clamp(err.z, -75, 75);
+ lab.add(err);
+ rgb = CU.colorPtToFFRGB(toRGB(lab));
+ }
+ Integer key = Integer.valueOf(rgb);
+ ColorCell cell = colorMap.get(key);
+ if (cell == null) {
+ // critical to generate normalized L*a*b from RGB here for nearestCell mapping.
+ // otherwise future RGB keys may match the wrong cell
+ lab = toLABnorm(rgb);
+ cell = nearestCell.get(key);
+ if (cell == null) {
+ // find nearest cell
+ float maxerr = Float.MAX_VALUE;
+ // skip 0 0 0
+ for (int ib = cells.size(); --ib >= 1;) {
+ ColorCell c = cells.get(ib);
+ err.sub2(lab, c.center);
+ float d = err.lengthSquared();
+ if (d < maxerr) {
+ maxerr = d;
+ cell = c;
+ }
+ }
+ nearestCell.put(key, cell);
+ }
+ if (floydSteinberg) {
+ // dither
+ err.sub2(lab, cell.center);
+ boolean notLastCol = (j < width - 1);
+ if (notLastCol)
+ addError(err, 7, errors, p + 1, w2);
+ if (notLastRow) {
+ if (j > 0)
+ addError(err, 3, errors, p + width - 1, w2);
+ addError(err, 5, errors, p + width, w2);
+ if (notLastCol)
+ addError(err, 1, errors, p + width + 1, w2);
+ }
+ }
+ err.x = Float.MAX_VALUE; // used; flag for resetting to 0
+ }
+ newPixels[p] = cell.index;
+ }
+ }
+ return newPixels;
+ }
+
+ private void addError(P3 err, int f, P3[] errors, int p, int w2) {
+ // GIMP will allow changing the background color.
+ if (pixels[p] == backgroundColor)
+ return;
+ p %= w2;
+ P3 errp = errors[p];
+ if (errp == null)
+ errp = errors[p] = new P3();
+ else if (errp.x == Float.MAX_VALUE) // reuse
+ errp.set(0, 0, 0);
+ errp.scaleAdd2(f / 16f, err, errp);
+ }
+
+ ///////////////////////// CIE L*a*b / XYZ / sRGB conversion methods /////////
+
+ // these could be static, but that just makes for more JavaScript code
+
+ protected P3 toLABnorm(int rgb) {
+ P3 lab = CU.colorPtFromInt(rgb, null);
+ rgbToXyz(lab, lab);
+ xyzToLab(lab, lab);
+ // normalize to 0-100
+ lab.y = (lab.y + 86.185f) / (98.254f + 86.185f) * 100f;
+ lab.z = (lab.z + 107.863f) / (94.482f + 107.863f) * 100f;
+ return lab;
+ }
+
+ protected P3 toRGB(P3 lab) {
+ P3 xyz = P3.newP(lab);
+ // normalized to 0-100
+ xyz.y = xyz.y / 100f * (98.254f + 86.185f) - 86.185f;
+ xyz.z = xyz.z / 100f * (94.482f + 107.863f) - 107.863f;
+ labToXyz(xyz, xyz);
+ return xyzToRgb(xyz, xyz);
+ }
+
+ private static M3 xyz2rgb;
+ private static M3 rgb2xyz;
+
+ static {
+ rgb2xyz = M3.newA9(new float[] { 0.4124f, 0.3576f, 0.1805f, 0.2126f,
+ 0.7152f, 0.0722f, 0.0193f, 0.1192f, 0.9505f });
+
+ xyz2rgb = M3.newA9(new float[] { 3.2406f, -1.5372f, -0.4986f, -0.9689f,
+ 1.8758f, 0.0415f, 0.0557f, -0.2040f, 1.0570f });
+ }
+
+ public P3 rgbToXyz(P3 rgb, P3 xyz) {
+ // http://en.wikipedia.org/wiki/CIE_1931_color_space
+ // http://rsb.info.nih.gov/ij/plugins/download/Color_Space_Converter.java
+ if (xyz == null)
+ xyz = new P3();
+ xyz.x = sxyz(rgb.x);
+ xyz.y = sxyz(rgb.y);
+ xyz.z = sxyz(rgb.z);
+ rgb2xyz.rotate(xyz);
+ return xyz;
+ }
+
+ private float sxyz(float x) {
+ x /= 255;
+ return (float) (x <= 0.04045 ? x / 12.92 : Math.pow(((x + 0.055) / 1.055),
+ 2.4)) * 100;
+ }
+
+ public P3 xyzToRgb(P3 xyz, P3 rgb) {
+ // http://en.wikipedia.org/wiki/CIE_1931_color_space
+ // http://rsb.info.nih.gov/ij/plugins/download/Color_Space_Converter.java
+ if (rgb == null)
+ rgb = new P3();
+ rgb.setT(xyz);
+ rgb.scale(0.01f);
+ xyz2rgb.rotate(rgb);
+ rgb.x = clamp(srgb(rgb.x), 0, 255);
+ rgb.y = clamp(srgb(rgb.y), 0, 255);
+ rgb.z = clamp(srgb(rgb.z), 0, 255);
+ return rgb;
+ }
+
+ private float srgb(float x) {
+ return (float) (x > 0.0031308f ? (1.055 * Math.pow(x, 1.0 / 2.4)) - 0.055
+ : x * 12.92) * 255;
+ }
+
+ public P3 xyzToLab(P3 xyz, P3 lab) {
+ // http://en.wikipedia.org/wiki/Lab_color_space
+ // http://rsb.info.nih.gov/ij/plugins/download/Color_Space_Converter.java
+ // Lab([0..100], [-86.185..98.254], [-107.863..94.482])
+ // XYZn = D65 = {95.0429, 100.0, 108.8900};
+ if (lab == null)
+ lab = new P3();
+ float x = flab(xyz.x / 95.0429f);
+ float y = flab(xyz.y / 100);
+ float z = flab(xyz.z / 108.89f);
+ lab.x = (116 * y) - 16;
+ lab.y = 500 * (x - y);
+ lab.z = 200 * (y - z);
+ return lab;
+ }
+
+ private float flab(float t) {
+ return (float) (t > 8.85645168E-3 /* (24/116)^3 */? Math.pow(t,
+ 0.333333333) : 7.78703704 /* 1/3*116/24*116/24 */* t + 0.137931034 /* 16/116 */
+ );
+ }
+
+ public P3 labToXyz(P3 lab, P3 xyz) {
+ // http://en.wikipedia.org/wiki/Lab_color_space
+ // http://rsb.info.nih.gov/ij/plugins/download/Color_Space_Converter.java
+ // XYZn = D65 = {95.0429, 100.0, 108.8900};
+ if (xyz == null)
+ xyz = new P3();
+
+ xyz.setT(lab);
+ float y = (xyz.x + 16) / 116;
+ float x = xyz.y / 500 + y;
+ float z = y - xyz.z / 200;
+ xyz.x = fxyz(x) * 95.0429f;
+ xyz.y = fxyz(y) * 100;
+ xyz.z = fxyz(z) * 108.89f;
+
+ return xyz;
+ }
+
+ private float fxyz(float t) {
+ return (float) (t > 0.206896552 /* (24/116) */? t * t * t
+ : 0.128418549 /* 3*24/116*24/116 */* (t - 0.137931034 /* 16/116 */));
+ }
+
+ private float clamp(float c, float min, float max) {
+ c = (c < min ? min : c > max ? max : c);
+ return (min == 0 ? Math.round(c) : c);
+ }
+
+ ///////////////////////// GifEncoder writing methods ////////////////////////
+
+ /**
+ * includes logical screen descriptor
+ *
+ * @throws IOException
+ */
+ private void writeHeader() throws IOException {
+ putString("GIF89a");
+ putWord(width);
+ putWord(height);
+ putByte(0); // no global color table -- using local instead
+ putByte(0); // no background
+ putByte(0); // no pixel aspect ratio given
+ }
+
+ private void writeGraphicControlExtension() {
+ if (isTransparent || delayTime100ths >= 0) {
+ putByte(0x21); // graphic control extension
+ putByte(0xf9); // graphic control label
+ putByte(4); // block size
+ putByte((isTransparent ? 9 : 0) | (delayTime100ths > 0 ? 2 : 0)); // packed bytes
+ putWord(delayTime100ths > 0 ? delayTime100ths : 0);
+ putByte(0); // transparent index
+ putByte(0); // end-of-block
+ }
+ }
+
+ // see http://www.vurdalakov.net/misc/gif/netscape-looping-application-extension
+ // +---------------+
+ // 0 | 0x21 | Extension Label
+ // +---------------+
+ // 1 | 0xFF | Application Extension Label
+ // +---------------+
+ // 2 | 0x0B | Block Size
+ // +---------------+
+ // 3 | |
+ // +- -+
+ // 4 | |
+ // +- -+
+ // 5 | |
+ // +- -+
+ // 6 | |
+ // +- NETSCAPE -+ Application Identifier (8 bytes)
+ // 7 | |
+ // +- -+
+ // 8 | |
+ // +- -+
+ // 9 | |
+ // +- -+
+ // 10 | |
+ // +---------------+
+ // 11 | |
+ // +- -+
+ // 12 | 2.0 | Application Authentication Code (3 bytes)
+ // +- -+
+ // 13 | |
+ // +===============+ --+
+ // 14 | 0x03 | Sub-block Data Size |
+ // +---------------+ |
+ // 15 | 0x01 | Sub-block ID |
+ // +---------------+ | Application Data Sub-block
+ // 16 | | |
+ // +- -+ Loop Count (2 bytes) |
+ // 17 | | |
+ // +===============+ --+
+ // 18 | 0x00 | Block Terminator
+ // +---------------+
+
+ private void writeNetscapeLoopExtension() {
+ putByte(0x21); // graphic control extension
+ putByte(0xff); // netscape loop extension
+ putByte(0x0B); // block size
+ putString("NETSCAPE2.0");
+ putByte(3);
+ putByte(1);
+ putWord(0); // loop indefinitely
+ putByte(0); // end-of-block
+
+ }
+
+ private int initCodeSize;
+ private int curpt;
+
+ private void writeImage() {
+ putByte(0x2C);
+ putWord(0); //left
+ putWord(0); //top
+ putWord(width);
+ putWord(height);
+
+ // <Packed Fields> = LISx xZZZ
+
+ // L Local Color Table Flag
+ // I Interlace Flag
+ // S Sort Flag
+ // x Reserved
+ // ZZZ Size of Local Color Table
+
+ int packedFields = 0x80 | (interlaced ? 0x40 : 0) | (bitsPerPixel - 1);
+ putByte(packedFields);
+ int colorMapSize = 1 << bitsPerPixel;
+ P3 p = new P3();
+ for (int i = 0; i < colorMapSize; i++) {
+ if (palette[i] != null)
+ p = palette[i];
+ putByte((int) p.x);
+ putByte((int) p.y);
+ putByte((int) p.z);
+ }
+ putByte(initCodeSize = (bitsPerPixel <= 1 ? 2 : bitsPerPixel));
+ compress();
+ putByte(0);
+ }
+
+ private void writeTrailer() {
+ // Write the GIF file terminator
+ putByte(0x3B);
+ }
+
+ ///// compression routines /////
+
+ private static final int EOF = -1;
+
+ // Return the next pixel from the image
+ private int nextPixel() {
+ if (countDown-- == 0)
+ return EOF;
+ int colorIndex = pixels[curpt];
+ // Bump the current X position
+ ++curx;
+ if (curx == width) {
+ // If we are at the end of a scan line, set curx back to the beginning
+ // If we are interlaced, bump the cury to the appropriate spot,
+ // otherwise, just increment it.
+ curx = 0;
+ if (interlaced)
+ updateY(INTERLACE_PARAMS[pass], INTERLACE_PARAMS[pass + 4]);
+ else
+ ++cury;
+ }
+ curpt = cury * width + curx;
+ return colorIndex & 0xff;
+ }
+
+ private static final int[] INTERLACE_PARAMS = { 8, 8, 4, 2, 4, 2, 1, 0 };
+
+ /**
+ *
+ * Group 1 : Every 8th. row, starting with row 0. (Pass 1)
+ *
+ * Group 2 : Every 8th. row, starting with row 4. (Pass 2)
+ *
+ * Group 3 : Every 4th. row, starting with row 2. (Pass 3)
+ *
+ * Group 4 : Every 2nd. row, starting with row 1. (Pass 4)
+ *
+ * @param yNext
+ * @param yNew
+ */
+ private void updateY(int yNext, int yNew) {
+ cury += yNext;
+ if (yNew >= 0 && cury >= height) {
+ cury = yNew;
+ ++pass;
+ }
+ }
+
+ // Write out a word to the GIF file
+ private void putWord(int w) {
+ putByte(w);
+ putByte(w >> 8);
+ }
+
+ // GIFCOMPR.C - GIF Image compression routines
+ //
+ // Lempel-Ziv compression based on 'compress'. GIF modifications by
+ // David Rowley (mgardi@watdcsu.waterloo.edu)
+
+ // General DEFINEs
+
+ private static final int BITS = 12;
+
+ private static final int HSIZE = 5003; // 80% occupancy
+
+ // GIF Image compression - modified 'compress'
+ //
+ // Based on: compress.c - File compression ala IEEE Computer, June 1984.
+ //
+ // By Authors: Spencer W. Thomas (decvax!harpo!utah-cs!utah-gr!thomas)
+ // Jim McKie (decvax!mcvax!jim)
+ // Steve Davies (decvax!vax135!petsd!peora!srd)
+ // Ken Turkowski (decvax!decwrl!turtlevax!ken)
+ // James A. Woods (decvax!ihnp4!ames!jaw)
+ // Joe Orost (decvax!vax135!petsd!joe)
+
+ private int nBits; // number of bits/code
+ private int maxbits = BITS; // user settable max # bits/code
+ private int maxcode; // maximum code, given n_bits
+ private int maxmaxcode = 1 << BITS; // should NEVER generate this code
+
+ private final static int MAXCODE(int nBits) {
+ return (1 << nBits) - 1;
+ }
+
+ private int[] htab = new int[HSIZE];
+ private int[] codetab = new int[HSIZE];
+
+ private int hsize = HSIZE; // for dynamic table sizing
+
+ private int freeEnt = 0; // first unused entry
+
+ // block compression parameters -- after all codes are used up,
+ // and compression rate changes, start over.
+ private boolean clearFlag = false;
+
+ // Algorithm: use open addressing double hashing (no chaining) on the
+ // prefix code / next character combination. We do a variant of Knuth's
+ // algorithm D (vol. 3, sec. 6.4) along with G. Knott's relatively-prime
+ // secondary probe. Here, the modular division first probe is gives way
+ // to a faster exclusive-or manipulation. Also do block compression with
+ // an adaptive reset, whereby the code table is cleared when the compression
+ // ratio decreases, but after the table fills. The variable-length output
+ // codes are re-sized at this point, and a special CLEAR code is generated
+ // for the decompressor. Late addition: construct the table according to
+ // file size for noticeable speed improvement on small files. Please direct
+ // questions about this implementation to ames!jaw.
+
+ private int clearCode;
+ private int EOFCode;
+
+ private int countDown;
+ private int pass = 0;
+ private int curx, cury;
+
+ private void compress() {
+
+ // Calculate number of bits we are expecting
+ countDown = width * height;
+
+ // Indicate which pass we are on (if interlace)
+ pass = 0;
+ // Set up the current x and y position
+ curx = 0;
+ cury = 0;
+
+ // Set up the necessary values
+ clearFlag = false;
+ nBits = initCodeSize + 1;
+ maxcode = MAXCODE(nBits);
+
+ clearCode = 1 << initCodeSize;
+ EOFCode = clearCode + 1;
+ freeEnt = clearCode + 2;
+
+ // Set up the 'byte output' routine
+ bufPt = 0;
+
+ int ent = nextPixel();
+
+ int hshift = 0;
+ int fcode;
+ for (fcode = hsize; fcode < 65536; fcode *= 2)
+ ++hshift;
+ hshift = 8 - hshift; // set hash code range bound
+
+ int hsizeReg = hsize;
+ clearHash(hsizeReg); // clear hash table
+
+ output(clearCode);
+
+ int c;
+ outer_loop: while ((c = nextPixel()) != EOF) {
+ fcode = (c << maxbits) + ent;
+ int i = (c << hshift) ^ ent; // xor hashing
+
+ if (htab[i] == fcode) {
+ ent = codetab[i];
+ continue;
+ } else if (htab[i] >= 0) // non-empty slot
+ {
+ int disp = hsizeReg - i; // secondary hash (after G. Knott)
+ if (i == 0)
+ disp = 1;
+ do {
+ if ((i -= disp) < 0)
+ i += hsizeReg;
+
+ if (htab[i] == fcode) {
+ ent = codetab[i];
+ continue outer_loop;
+ }
+ } while (htab[i] >= 0);
+ }
+ output(ent);
+ ent = c;
+ if (freeEnt < maxmaxcode) {
+ codetab[i] = freeEnt++; // code -> hashtable
+ htab[i] = fcode;
+ } else {
+ clearBlock();
+ }
+ }
+ // Put out the final code.
+ output(ent);
+ output(EOFCode);
+ }
+
+ // output
+ //
+ // Output the given code.
+ // Inputs:
+ // code: A n_bits-bit integer. If == -1, then EOF. This assumes
+ // that n_bits =< wordsize - 1.
+ // Outputs:
+ // Outputs code to the file.
+ // Assumptions:
+ // Chars are 8 bits long.
+ // Algorithm:
+ // Maintain a BITS character long buffer (so that 8 codes will
+ // fit in it exactly). Use the VAX insv instruction to insert each
+ // code in turn. When the buffer fills up empty it and start over.
+
+ private int curAccum = 0;
+ private int curBits = 0;
+
+ private int masks[] = { 0x0000, 0x0001, 0x0003, 0x0007, 0x000F, 0x001F,
+ 0x003F, 0x007F, 0x00FF, 0x01FF, 0x03FF, 0x07FF, 0x0FFF, 0x1FFF, 0x3FFF,
+ 0x7FFF, 0xFFFF };
+
+ private void output(int code) {
+ curAccum &= masks[curBits];
+
+ if (curBits > 0)
+ curAccum |= (code << curBits);
+ else
+ curAccum = code;
+
+ curBits += nBits;
+
+ while (curBits >= 8) {
+ byteOut((byte) (curAccum & 0xff));
+ curAccum >>= 8;
+ curBits -= 8;
+ }
+
+ // If the next entry is going to be too big for the code size,
+ // then increase it, if possible.
+ if (freeEnt > maxcode || clearFlag) {
+ if (clearFlag) {
+ maxcode = MAXCODE(nBits = initCodeSize + 1);
+ clearFlag = false;
+ } else {
+ ++nBits;
+ if (nBits == maxbits)
+ maxcode = maxmaxcode;
+ else
+ maxcode = MAXCODE(nBits);
+ }
+ }
+
+ if (code == EOFCode) {
+ // At EOF, write the rest of the buffer.
+ while (curBits > 0) {
+ byteOut((byte) (curAccum & 0xff));
+ curAccum >>= 8;
+ curBits -= 8;
+ }
+ flushBytes();
+ }
+ }
+
+ // Clear out the hash table
+
+ // table clear for block compress
+ private void clearBlock() {
+ clearHash(hsize);
+ freeEnt = clearCode + 2;
+ clearFlag = true;
+
+ output(clearCode);
+ }
+
+ // reset code table
+ private void clearHash(int hsize) {
+ for (int i = 0; i < hsize; ++i)
+ htab[i] = -1;
+ }
+
+ // GIF-specific routines (byte array buffer)
+
+ // Number of bytes so far in this 'packet'
+ private int bufPt;
+
+ // Define the storage for the packet accumulator
+ final private byte[] buf = new byte[256];
+
+ // Add a byte to the end of the current packet, and if it is 254
+ // byte, flush the packet to disk.
+ private void byteOut(byte c) {
+ buf[bufPt++] = c;
+ if (bufPt >= 254)
+ flushBytes();
+ }
+
+ // Flush the packet to disk, and reset the accumulator
+ protected void flushBytes() {
+ if (bufPt > 0) {
+ putByte(bufPt);
+ out.write(buf, 0, bufPt);
+ byteCount += bufPt;
+ bufPt = 0;
+ }
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-06-02 12:14:13 -0500 (Sat, 02 Jun 2007) $
+ * $Revision: 7831 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2000-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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.
+ */
+
+// ImageEncoder - abstract class for writing out an image
+//
+// Copyright (C) 1996 by Jef Poskanzer <jef@mail.acme.com>. All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+// OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+// HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+//
+// Visit the ACME Labs Java page for up-to-date versions of this and other
+// fine Java utilities: http://www.acme.com/java/
+
+package javajs.img;
+
+import java.util.Map;
+
+import javajs.api.GenericImageEncoder;
+import javajs.util.OC;
+
+
+
+/**
+ * Generic abstract image creator:
+ *
+ * (1) set parameters
+ *
+ * (2) encode the image bytes, if necessary
+ *
+ * (3) generate the image
+ * @author Bob Hanson hansonr@stolaf.edu
+ */
+
+public abstract class ImageEncoder implements GenericImageEncoder {
+
+ protected OC out;
+
+ protected int width = -1;
+ protected int height = -1;
+ protected int quality = -1;
+ protected String date;
+ protected boolean logging;
+ protected boolean doClose = true;
+
+ /**
+ * @param type
+ * @param out
+ * @param params
+ */
+ @Override
+ public boolean createImage(String type, OC out, Map<String, Object> params)
+ throws Exception {
+ this.out = out;
+ logging = (Boolean.TRUE == params.get("logging"));
+ width = ((Integer) params.get("imageWidth")).intValue();
+ height = ((Integer) params.get("imageHeight")).intValue();
+ pixels = (int[]) params.get("imagePixels");
+ date = (String) params.get("date");
+ Integer q = (Integer) params.get("quality");
+ quality = (q == null ? -1 : q.intValue());
+ setParams(params);
+ generate();
+ close(); // GIF will override this and not close
+ return doClose;
+ }
+
+ abstract protected void setParams(Map<String, Object> params);
+ abstract protected void generate() throws Exception;
+
+ protected int[] pixels;
+
+ protected void putString(String s) {
+ byte[] b = s.getBytes();
+ out.write(b, 0, b.length);
+ }
+
+ protected void putByte(int b) {
+ out.writeByteAsInt(b);
+ }
+
+ protected void close() {
+ // your responsibility to close the output channel
+ }
+
+}
--- /dev/null
+// Version 1.0a
+// Copyright (C) 1998, James R. Weeks and BioElectroMech.
+// Visit BioElectroMech at www.obrador.com. Email James@obrador.com.
+
+// See license.txt for details about the allowed used of this software.
+// This software is based in part on the work of the Independent JPEG Group.
+// See IJGreadme.txt for details about the Independent JPEG Group's license.
+
+// This encoder is inspired by the Java Jpeg encoder by Florian Raemy,
+// studwww.eurecom.fr/~raemy.
+// It borrows a great deal of code and structure from the Independent
+// Jpeg Group's Jpeg 6a library, Copyright Thomas G. Lane.
+// See license.txt for details
+
+/*
+ * JpegEncoder and its associated classes are Copyright (c) 1998, James R. Weeks and BioElectroMech
+ * see(Jmol/src/com/obrador/license.txt)
+ *
+ * javajs.img.JpegEncoder.java was adapted by Bob Hanson
+ * for Jmol in the following ways:
+ *
+ * 1) minor coding efficiencies were made in some for() loops.
+ * 2) methods not used by Jmol were commented out
+ * 3) method and variable signatures were modified to provide
+ * more appropriate method privacy.
+ * 4) additions for Java2Script compatibility
+ *
+ * Original files are maintained in the Jmol.src.com.obrador package, but
+ * these original files are not distributed with Jmol.
+ *
+*/
+
+package javajs.img;
+
+import java.io.IOException;
+import java.util.Map;
+
+import javajs.util.Base64;
+import javajs.util.OC;
+
+
+public class Jpg64Encoder extends JpgEncoder {
+
+ private OC outTemp;
+
+ @Override
+ protected void setParams(Map<String, Object> params) {
+ defaultQuality = 75;
+ outTemp = (OC) params.remove("outputChannelTemp");
+ super.setParams(params);
+ }
+
+ @Override
+ protected void generate() throws IOException {
+ OC out0 = out;
+ out = outTemp;
+ super.generate();
+ byte[] bytes = Base64.getBytes64(out.toByteArray());
+ outTemp = null;
+ out = out0;
+ out.write(bytes, 0, bytes.length);
+ }
+
+}
--- /dev/null
+// Version 1.0a
+// Copyright (C) 1998, James R. Weeks and BioElectroMech.
+// Visit BioElectroMech at www.obrador.com. Email James@obrador.com.
+
+// See license.txt for details about the allowed used of this software.
+// This software is based in part on the work of the Independent JPEG Group.
+// See IJGreadme.txt for details about the Independent JPEG Group's license.
+
+// This encoder is inspired by the Java Jpeg encoder by Florian Raemy,
+// studwww.eurecom.fr/~raemy.
+// It borrows a great deal of code and structure from the Independent
+// Jpeg Group's Jpeg 6a library, Copyright Thomas G. Lane.
+// See license.txt for details
+
+/*
+ * JpegEncoder and its associated classes are Copyright (c) 1998, James R. Weeks and BioElectroMech
+ * see(Jmol/src/com/obrador/license.txt)
+ *
+ * javjs.img.JpegEncoder.java was adapted by Bob Hanson
+ *
+ * for Jmol in the following ways:
+ *
+ * 1) minor coding efficiencies were made in some for() loops.
+ * 2) methods not used by Jmol were commented out
+ * 3) method and variable signatures were modified to provide
+ * more appropriate method privacy.
+ * 4) additions for Java2Script compatibility
+ *
+ * Original files are maintained in the Jmol.src.com.obrador package, but
+ * these original files are not distributed with Jmol.
+ *
+*/
+
+package javajs.img;
+
+import java.io.IOException;
+import java.util.Map;
+
+import javajs.img.ImageEncoder;
+import javajs.util.AU;
+import javajs.util.OC;
+
+/**
+ * JpegEncoder - The JPEG main program which performs a jpeg compression of an
+ * image.
+ *
+ * A system to allow the full Jmol state -- regardless of length --
+ * to be encoded in a set of APP1 (FFE1) tags.
+ * But we have to be careful about line ends for backward compatibility.
+ * This solution is not 100% effective, because some data lines may in principle be
+ * Very large and may not contain new lines for more than 65500 characters,
+ * But that would be very unusual. Perhaps a huge data set loaded from a
+ * string. Introduced in Jmol 12.1.36. Bob Hanson
+ *
+ * See org.com.obrador.license.txt
+ *
+ */
+
+public class JpgEncoder extends ImageEncoder {
+
+ // this string will GENERALLY appear at the end of lines and be escaped
+ private static final int CONTINUE_MAX = 65500; // some room to spare here.
+ private static final int CONTINUE_MAX_BUFFER = CONTINUE_MAX + 10; // never break up last 10 bytes
+
+ private JpegObj jpegObj;
+ private Huffman huf;
+ private DCT dct;
+ protected int defaultQuality = 100;
+ private String applicationTag;
+
+ public JpgEncoder() {
+
+ }
+
+ @Override
+ protected void setParams(Map<String, Object> params) {
+ if (quality <= 0)
+ quality = (params.containsKey("qualityJPG") ? ((Integer) params.get("qualityJPG")).intValue() : defaultQuality);
+ jpegObj = new JpegObj();
+ jpegObj.comment = (String) params.get("comment");
+ applicationTag = (String) params.get("jpgAppTag");
+ }
+
+ @Override
+ protected void generate() throws IOException {
+ jpegObj.imageWidth = width;
+ jpegObj.imageHeight = height;
+ dct = new DCT(quality);
+ huf = new Huffman(width, height);
+ if (jpegObj == null)
+ return;
+ jpegObj.getYCCArray(pixels);
+ String longState = writeHeaders(jpegObj, dct);
+ writeCompressedData(jpegObj, dct, huf);
+ writeMarker(eoi);
+ if (longState != null) {
+ byte[] b = longState.getBytes();
+ out.write(b, 0, b.length);
+ }
+ }
+
+ private void writeCompressedData(JpegObj jpegObj, DCT dct, Huffman huf) {
+ int i, j, r, c, a, b;
+ int comp, xpos, ypos, xblockoffset, yblockoffset;
+ float inputArray[][];
+ float dctArray1[][] = new float[8][8];
+ double dctArray2[][] = new double[8][8];
+ int dctArray3[] = new int[8 * 8];
+
+ /*
+ * This method controls the compression of the image.
+ * Starting at the upper left of the image, it compresses 8x8 blocks
+ * of data until the entire image has been compressed.
+ */
+
+ int lastDCvalue[] = new int[jpegObj.numberOfComponents];
+ //int zeroArray[] = new int[64]; // initialized to hold all zeros
+ //int Width = 0, Height = 0;
+ //int nothing = 0, not;
+ int minBlockWidth, minBlockHeight;
+ // This initial setting of MinBlockWidth and MinBlockHeight is done to
+ // ensure they start with values larger than will actually be the case.
+ minBlockWidth = ((huf.imageWidth % 8 != 0) ? (int) (Math
+ .floor(huf.imageWidth / 8.0) + 1) * 8 : huf.imageWidth);
+ minBlockHeight = ((huf.imageHeight % 8 != 0) ? (int) (Math
+ .floor(huf.imageHeight / 8.0) + 1) * 8 : huf.imageHeight);
+ for (comp = 0; comp < jpegObj.numberOfComponents; comp++) {
+ minBlockWidth = Math.min(minBlockWidth, jpegObj.blockWidth[comp]);
+ minBlockHeight = Math.min(minBlockHeight, jpegObj.blockHeight[comp]);
+ }
+ xpos = 0;
+ for (r = 0; r < minBlockHeight; r++) {
+ for (c = 0; c < minBlockWidth; c++) {
+ xpos = c * 8;
+ ypos = r * 8;
+ for (comp = 0; comp < jpegObj.numberOfComponents; comp++) {
+ //Width = JpegObj.BlockWidth[comp];
+ //Height = JpegObj.BlockHeight[comp];
+ inputArray = jpegObj.components[comp];
+ int vsampF = jpegObj.vsampFactor[comp];
+ int hsampF = jpegObj.hsampFactor[comp];
+ int qNumber = jpegObj.qtableNumber[comp];
+ int dcNumber = jpegObj.dctableNumber[comp];
+ int acNumber = jpegObj.actableNumber[comp];
+
+ for (i = 0; i < vsampF; i++) {
+ for (j = 0; j < hsampF; j++) {
+ xblockoffset = j * 8;
+ yblockoffset = i * 8;
+ for (a = 0; a < 8; a++) {
+ for (b = 0; b < 8; b++) {
+
+ // I believe this is where the dirty line at the bottom of
+ // the image is coming from.
+ // I need to do a check here to make sure I'm not reading past
+ // image data.
+ // This seems to not be a big issue right now. (04/04/98)
+
+ dctArray1[a][b] = inputArray[ypos + yblockoffset + a][xpos
+ + xblockoffset + b];
+ }
+ }
+ // The following code commented out because on some images this technique
+ // results in poor right and bottom borders.
+ // if ((!JpegObj.lastColumnIsDummy[comp] || c < Width - 1) &&
+ // (!JpegObj.lastRowIsDummy[comp] || r < Height - 1)) {
+ dctArray2 = DCT.forwardDCT(dctArray1);
+ dctArray3 = DCT.quantizeBlock(dctArray2, dct.divisors[qNumber]);
+ // }
+ // else {
+ // zeroArray[0] = dctArray3[0];
+ // zeroArray[0] = lastDCvalue[comp];
+ // dctArray3 = zeroArray;
+ // }
+ huf.HuffmanBlockEncoder(out, dctArray3, lastDCvalue[comp],
+ dcNumber, acNumber);
+ lastDCvalue[comp] = dctArray3[0];
+ }
+ }
+ }
+ }
+ }
+ huf.flushBuffer(out);
+ }
+
+ private static byte[] eoi = { (byte) 0xFF, (byte) 0xD9 };
+
+ private static byte[] jfif = new byte[] {
+ /* JFIF[0] =*/(byte) 0xff,
+ /* JFIF[1] =*/(byte) 0xe0,
+ /* JFIF[2] =*/0,
+ /* JFIF[3] =*/16,
+ /* JFIF[4] =*/(byte) 0x4a, //'J'
+ /* JFIF[5] =*/(byte) 0x46, //'F'
+ /* JFIF[6] =*/(byte) 0x49, //'I'
+ /* JFIF[7] =*/(byte) 0x46, //'F'
+ /* JFIF[8] =*/0,
+ /* JFIF[9] =*/1,
+ /* JFIF[10] =*/0,
+ /* JFIF[11] =*/0,
+ /* JFIF[12] =*/0,
+ /* JFIF[13] =*/1,
+ /* JFIF[14] =*/0,
+ /* JFIF[15] =*/1,
+ /* JFIF[16] =*/0,
+ /* JFIF[17] =*/0 };
+
+ private static byte[] soi = { (byte) 0xFF, (byte) 0xD8 };
+
+ private String writeHeaders(JpegObj jpegObj, DCT dct) {
+ int i, j, index, offset;
+ int tempArray[];
+
+ // the SOI marker
+ writeMarker(soi);
+
+ // The order of the following headers is quite inconsequential.
+ // the JFIF header
+ writeArray(jfif);
+
+ // Comment Header
+ String comment = null;
+ if (jpegObj.comment != null && jpegObj.comment.length() > 0)
+ writeString(jpegObj.comment, (byte) 0xE1); // App data 1
+ writeString(
+ "JPEG Encoder Copyright 1998, James R. Weeks and BioElectroMech.\n\n",
+ (byte) 0xFE);
+
+ // The DQT header
+ // 0 is the luminance index and 1 is the chrominance index
+ byte dqt[] = new byte[134];
+ dqt[0] = (byte) 0xFF;
+ dqt[1] = (byte) 0xDB;
+ dqt[2] = 0;
+ dqt[3] = (byte) 132;
+ offset = 4;
+ for (i = 0; i < 2; i++) {
+ dqt[offset++] = (byte) ((0 << 4) + i);
+ tempArray = dct.quantum[i];
+ for (j = 0; j < 64; j++) {
+ dqt[offset++] = (byte) tempArray[Huffman.jpegNaturalOrder[j]];
+ }
+ }
+ writeArray(dqt);
+
+ // Start of Frame Header
+ byte sof[] = new byte[19];
+ sof[0] = (byte) 0xFF;
+ sof[1] = (byte) 0xC0;
+ sof[2] = 0;
+ sof[3] = 17;
+ sof[4] = (byte) jpegObj.precision;
+ sof[5] = (byte) ((jpegObj.imageHeight >> 8) & 0xFF);
+ sof[6] = (byte) ((jpegObj.imageHeight) & 0xFF);
+ sof[7] = (byte) ((jpegObj.imageWidth >> 8) & 0xFF);
+ sof[8] = (byte) ((jpegObj.imageWidth) & 0xFF);
+ sof[9] = (byte) jpegObj.numberOfComponents;
+ index = 10;
+ for (i = 0; i < sof[9]; i++) {
+ sof[index++] = (byte) jpegObj.compID[i];
+ sof[index++] = (byte) ((jpegObj.hsampFactor[i] << 4) + jpegObj.vsampFactor[i]);
+ sof[index++] = (byte) jpegObj.qtableNumber[i];
+ }
+ writeArray(sof);
+
+ WriteDHTHeader(Huffman.bitsDCluminance, Huffman.valDCluminance);
+ WriteDHTHeader(Huffman.bitsACluminance, Huffman.valACluminance);
+ WriteDHTHeader(Huffman.bitsDCchrominance, Huffman.valDCchrominance);
+ WriteDHTHeader(Huffman.bitsACchrominance, Huffman.valACchrominance);
+
+ // Start of Scan Header
+ byte sos[] = new byte[14];
+ sos[0] = (byte) 0xFF;
+ sos[1] = (byte) 0xDA;
+ sos[2] = 0;
+ sos[3] = 12;
+ sos[4] = (byte) jpegObj.numberOfComponents;
+ index = 5;
+ for (i = 0; i < sos[4]; i++) {
+ sos[index++] = (byte) jpegObj.compID[i];
+ sos[index++] = (byte) ((jpegObj.dctableNumber[i] << 4) + jpegObj.actableNumber[i]);
+ }
+ sos[index++] = (byte) jpegObj.ss;
+ sos[index++] = (byte) jpegObj.se;
+ sos[index++] = (byte) ((jpegObj.ah << 4) + jpegObj.al);
+ writeArray(sos);
+ return comment;
+ }
+
+ private void writeString(String s, byte id) {
+ int len = s.length();
+ int i0 = 0;
+ String suffix = applicationTag;
+ while (i0 < len) {
+ int nBytes = len - i0;
+ if (nBytes > CONTINUE_MAX_BUFFER) {
+ nBytes = CONTINUE_MAX;
+ // but break only at line breaks
+ int pt = s.lastIndexOf('\n', i0 + nBytes);
+ if (pt > i0 + 1)
+ nBytes = pt - i0;
+ }
+ if (i0 + nBytes == len)
+ suffix = "";
+ writeTag(nBytes + suffix.length(), id);
+ writeArray(s.substring(i0, i0 + nBytes).getBytes());
+ if (suffix.length() > 0)
+ writeArray(suffix.getBytes());
+ i0 += nBytes;
+ }
+ }
+
+ private void writeTag(int length, byte id) {
+ length += 2;
+ byte com[] = new byte[4];
+ com[0] = (byte) 0xFF;
+ com[1] = id;
+ com[2] = (byte) ((length >> 8) & 0xFF);
+ com[3] = (byte) (length & 0xFF);
+ writeArray(com);
+ }
+
+ void WriteDHTHeader(int[] bits, int[] val) {
+ // hansonr@stolaf.edu: simplified code.
+ byte[] dht;
+ int bytes = 0;
+ for (int j = 1; j < 17; j++)
+ bytes += bits[j];
+ dht = new byte[21 + bytes];
+ dht[0] = (byte) 0xFF;
+ dht[1] = (byte) 0xC4;
+ int index = 4;
+ for (int j = 0; j < 17; j++)
+ dht[index++] = (byte) bits[j];
+ for (int j = 0; j < bytes; j++)
+ dht[index++] = (byte) val[j];
+ dht[2] = (byte) (((index - 2) >> 8) & 0xFF);
+ dht[3] = (byte) ((index - 2) & 0xFF);
+ writeArray(dht);
+ }
+
+ void writeMarker(byte[] data) {
+ out.write(data, 0, 2);
+ }
+
+ void writeArray(byte[] data) {
+ out.write(data, 0, data.length);
+ }
+
+}
+
+// This class incorporates quality scaling as implemented in the JPEG-6a
+// library.
+
+/*
+ * DCT - A Java implementation of the Discreet Cosine Transform
+ */
+
+class DCT {
+
+ /**
+ * DCT Block Size - default 8
+ */
+ private final static int N = 8;
+ private final static int NN = N * N;
+
+ /**
+ * Image Quality (0-100) - default 80 (good image / good compression)
+ */
+ //public int QUALITY = 80;
+
+ int[][] quantum = AU.newInt2(2);
+ double[][] divisors = AU.newDouble2(2);
+
+ /**
+ * Quantitization Matrix for luminace.
+ */
+ private int quantum_luminance[] = new int[NN];
+ private double DivisorsLuminance[] = new double[NN];
+
+ /**
+ * Quantitization Matrix for chrominance.
+ */
+ private int quantum_chrominance[] = new int[NN];
+ private double DivisorsChrominance[] = new double[NN];
+
+ /**
+ * Constructs a new DCT object. Initializes the cosine transform matrix these
+ * are used when computing the DCT and it's inverse. This also initializes the
+ * run length counters and the ZigZag sequence. Note that the image quality
+ * can be worse than 25 however the image will be extemely pixelated, usually
+ * to a block size of N.
+ *
+ * @param quality
+ * The quality of the image (0 worst - 100 best)
+ *
+ */
+ DCT(int quality) {
+ initMatrix(quality);
+ }
+
+ /*
+ * This method sets up the quantization matrix for luminance and
+ * chrominance using the Quality parameter.
+ */
+ private void initMatrix(int quality) {
+ // converting quality setting to that specified in the jpeg_quality_scaling
+ // method in the IJG Jpeg-6a C libraries
+
+ quality = (quality < 1 ? 1 : quality > 100 ? 100 : quality);
+ quality = (quality < 50 ? 5000 / quality : 200 - quality * 2);
+
+ // Creating the luminance matrix
+
+ quantum_luminance[0] = 16;
+ quantum_luminance[1] = 11;
+ quantum_luminance[2] = 10;
+ quantum_luminance[3] = 16;
+ quantum_luminance[4] = 24;
+ quantum_luminance[5] = 40;
+ quantum_luminance[6] = 51;
+ quantum_luminance[7] = 61;
+ quantum_luminance[8] = 12;
+ quantum_luminance[9] = 12;
+ quantum_luminance[10] = 14;
+ quantum_luminance[11] = 19;
+ quantum_luminance[12] = 26;
+ quantum_luminance[13] = 58;
+ quantum_luminance[14] = 60;
+ quantum_luminance[15] = 55;
+ quantum_luminance[16] = 14;
+ quantum_luminance[17] = 13;
+ quantum_luminance[18] = 16;
+ quantum_luminance[19] = 24;
+ quantum_luminance[20] = 40;
+ quantum_luminance[21] = 57;
+ quantum_luminance[22] = 69;
+ quantum_luminance[23] = 56;
+ quantum_luminance[24] = 14;
+ quantum_luminance[25] = 17;
+ quantum_luminance[26] = 22;
+ quantum_luminance[27] = 29;
+ quantum_luminance[28] = 51;
+ quantum_luminance[29] = 87;
+ quantum_luminance[30] = 80;
+ quantum_luminance[31] = 62;
+ quantum_luminance[32] = 18;
+ quantum_luminance[33] = 22;
+ quantum_luminance[34] = 37;
+ quantum_luminance[35] = 56;
+ quantum_luminance[36] = 68;
+ quantum_luminance[37] = 109;
+ quantum_luminance[38] = 103;
+ quantum_luminance[39] = 77;
+ quantum_luminance[40] = 24;
+ quantum_luminance[41] = 35;
+ quantum_luminance[42] = 55;
+ quantum_luminance[43] = 64;
+ quantum_luminance[44] = 81;
+ quantum_luminance[45] = 104;
+ quantum_luminance[46] = 113;
+ quantum_luminance[47] = 92;
+ quantum_luminance[48] = 49;
+ quantum_luminance[49] = 64;
+ quantum_luminance[50] = 78;
+ quantum_luminance[51] = 87;
+ quantum_luminance[52] = 103;
+ quantum_luminance[53] = 121;
+ quantum_luminance[54] = 120;
+ quantum_luminance[55] = 101;
+ quantum_luminance[56] = 72;
+ quantum_luminance[57] = 92;
+ quantum_luminance[58] = 95;
+ quantum_luminance[59] = 98;
+ quantum_luminance[60] = 112;
+ quantum_luminance[61] = 100;
+ quantum_luminance[62] = 103;
+ quantum_luminance[63] = 99;
+
+ AANscale(DivisorsLuminance, quantum_luminance, quality);
+
+ // Creating the chrominance matrix
+
+ for (int i = 4; i < 64; i++)
+ quantum_chrominance[i] = 99;
+
+ quantum_chrominance[0] = 17;
+ quantum_chrominance[1] = 18;
+ quantum_chrominance[2] = 24;
+ quantum_chrominance[3] = 47;
+
+ quantum_chrominance[8] = 18;
+ quantum_chrominance[9] = 21;
+ quantum_chrominance[10] = 26;
+ quantum_chrominance[11] = 66;
+
+ quantum_chrominance[16] = 24;
+ quantum_chrominance[17] = 26;
+ quantum_chrominance[18] = 56;
+
+ quantum_chrominance[24] = 47;
+ quantum_chrominance[25] = 66;
+
+ AANscale(DivisorsChrominance, quantum_chrominance, quality);
+
+ // quantum and Divisors are objects used to hold the appropriate matices
+
+ quantum[0] = quantum_luminance;
+ quantum[1] = quantum_chrominance;
+
+ divisors[0] = DivisorsLuminance;
+ divisors[1] = DivisorsChrominance;
+
+ }
+
+ private final static double[] AANscaleFactor = { 1.0, 1.387039845,
+ 1.306562965, 1.175875602, 1.0, 0.785694958, 0.541196100, 0.275899379 };
+
+ static private void AANscale(double[] divisors, int[] values, int quality) {
+
+ for (int j = 0; j < 64; j++) {
+ int temp = (values[j] * quality + 50) / 100;
+ values[j] = (temp < 1 ? 1 : temp > 255 ? 255 : temp);
+ }
+
+ for (int i = 0, index = 0; i < 8; i++)
+ for (int j = 0; j < 8; j++, index++)
+ // The divisors for the LL&M method (the slow integer method used in
+ // jpeg 6a library). This method is currently (04/04/98) incompletely
+ // implemented.
+ // DivisorsLuminance[index] = ((double) quantum_luminance[index]) << 3;
+ // The divisors for the AAN method (the float method used in jpeg 6a library.
+ divisors[index] = (0.125 / (values[index] * AANscaleFactor[i] * AANscaleFactor[j]));
+ }
+
+ /*
+ * This method preforms forward DCT on a block of image data using
+ * the literal method specified for a 2-D Discrete Cosine Transform.
+ * It is included as a curiosity and can give you an idea of the
+ * difference in the compression result (the resulting image quality)
+ * by comparing its output to the output of the AAN method below.
+ * It is ridiculously inefficient.
+ */
+
+ // For now the final output is unusable. The associated quantization step
+ // needs some tweaking. If you get this part working, please let me know.
+ /*
+ public double[][] forwardDCTExtreme(float input[][])
+ {
+ double output[][] = new double[N][N];
+ int v, u, x, y;
+ for (v = 0; v < 8; v++) {
+ for (u = 0; u < 8; u++) {
+ for (x = 0; x < 8; x++) {
+ for (y = 0; y < 8; y++) {
+ output[v][u] += input[x][y] *
+ Math.cos(((double)(2*x + 1)*(double)u*Math.PI)/16)*
+ Math.cos(((double)(2*y + 1)*(double)v*Math.PI)/16);
+ }
+ }
+ output[v][u] *= (0.25)*((u == 0) ? (1.0/Math.sqrt(2)) : (double) 1.0)*((v == 0) ? (1.0/Math.sqrt(2)) : (double) 1.0);
+ }
+ }
+ return output;
+ }
+
+ */
+ /*
+ * This method preforms a DCT on a block of image data using the AAN
+ * method as implemented in the IJG Jpeg-6a library.
+ */
+ static double[][] forwardDCT(float input[][]) {
+ double output[][] = new double[N][N];
+ double tmp0, tmp1, tmp2, tmp3, tmp4, tmp5, tmp6, tmp7;
+ double tmp10, tmp11, tmp12, tmp13;
+ double z1, z2, z3, z4, z5, z11, z13;
+ // Subtracts 128 from the input values
+ for (int i = 0; i < 8; i++)
+ for (int j = 0; j < 8; j++)
+ output[i][j] = (input[i][j] - 128.0);
+ // input[i][j] -= 128;
+
+ for (int i = 0; i < 8; i++) {
+ tmp0 = output[i][0] + output[i][7];
+ tmp7 = output[i][0] - output[i][7];
+ tmp1 = output[i][1] + output[i][6];
+ tmp6 = output[i][1] - output[i][6];
+ tmp2 = output[i][2] + output[i][5];
+ tmp5 = output[i][2] - output[i][5];
+ tmp3 = output[i][3] + output[i][4];
+ tmp4 = output[i][3] - output[i][4];
+
+ tmp10 = tmp0 + tmp3;
+ tmp13 = tmp0 - tmp3;
+ tmp11 = tmp1 + tmp2;
+ tmp12 = tmp1 - tmp2;
+
+ output[i][0] = tmp10 + tmp11;
+ output[i][4] = tmp10 - tmp11;
+
+ z1 = (tmp12 + tmp13) * 0.707106781;
+ output[i][2] = tmp13 + z1;
+ output[i][6] = tmp13 - z1;
+
+ tmp10 = tmp4 + tmp5;
+ tmp11 = tmp5 + tmp6;
+ tmp12 = tmp6 + tmp7;
+
+ z5 = (tmp10 - tmp12) * 0.382683433;
+ z2 = 0.541196100 * tmp10 + z5;
+ z4 = 1.306562965 * tmp12 + z5;
+ z3 = tmp11 * 0.707106781;
+
+ z11 = tmp7 + z3;
+ z13 = tmp7 - z3;
+
+ output[i][5] = z13 + z2;
+ output[i][3] = z13 - z2;
+ output[i][1] = z11 + z4;
+ output[i][7] = z11 - z4;
+ }
+
+ for (int i = 0; i < 8; i++) {
+ tmp0 = output[0][i] + output[7][i];
+ tmp7 = output[0][i] - output[7][i];
+ tmp1 = output[1][i] + output[6][i];
+ tmp6 = output[1][i] - output[6][i];
+ tmp2 = output[2][i] + output[5][i];
+ tmp5 = output[2][i] - output[5][i];
+ tmp3 = output[3][i] + output[4][i];
+ tmp4 = output[3][i] - output[4][i];
+
+ tmp10 = tmp0 + tmp3;
+ tmp13 = tmp0 - tmp3;
+ tmp11 = tmp1 + tmp2;
+ tmp12 = tmp1 - tmp2;
+
+ output[0][i] = tmp10 + tmp11;
+ output[4][i] = tmp10 - tmp11;
+
+ z1 = (tmp12 + tmp13) * 0.707106781;
+ output[2][i] = tmp13 + z1;
+ output[6][i] = tmp13 - z1;
+
+ tmp10 = tmp4 + tmp5;
+ tmp11 = tmp5 + tmp6;
+ tmp12 = tmp6 + tmp7;
+
+ z5 = (tmp10 - tmp12) * 0.382683433;
+ z2 = 0.541196100 * tmp10 + z5;
+ z4 = 1.306562965 * tmp12 + z5;
+ z3 = tmp11 * 0.707106781;
+
+ z11 = tmp7 + z3;
+ z13 = tmp7 - z3;
+
+ output[5][i] = z13 + z2;
+ output[3][i] = z13 - z2;
+ output[1][i] = z11 + z4;
+ output[7][i] = z11 - z4;
+ }
+
+ return output;
+ }
+
+ /*
+ * This method quantitizes data and rounds it to the nearest integer.
+ */
+ static int[] quantizeBlock(double inputData[][], double[] divisorsCode) {
+ int outputData[] = new int[NN];
+ for (int i = 0, index = 0; i < 8; i++)
+ for (int j = 0; j < 8; j++, index++)
+ // The second line results in significantly better compression.
+ outputData[index] = (int) (Math.round(inputData[i][j]
+ * divisorsCode[index]));
+ // outputData[index] = (int)(((inputData[i][j] * (((double[]) (Divisors[code]))[index])) + 16384.5) -16384);
+ return outputData;
+ }
+
+ /*
+ * This is the method for quantizing a block DCT'ed with forwardDCTExtreme
+ * This method quantitizes data and rounds it to the nearest integer.
+ */
+
+ /*
+
+ public double[][] forwardDCTExtreme(float input[][])
+ {
+ double output[][] = new double[N][N];
+ int v, u, x, y;
+ for (v = 0; v < 8; v++) {
+ for (u = 0; u < 8; u++) {
+ for (x = 0; x < 8; x++) {
+ for (y = 0; y < 8; y++) {
+ output[v][u] += input[x][y] *
+ Math.cos(((double)(2*x + 1)*(double)u*Math.PI)/16)*
+ Math.cos(((double)(2*y + 1)*(double)v*Math.PI)/16);
+ }
+ }
+ output[v][u] *= (0.25)*((u == 0) ? (1.0/Math.sqrt(2)) : (double) 1.0)*((v == 0) ? (1.0/Math.sqrt(2)) : (double) 1.0);
+ }
+ }
+ return output;
+ }
+
+ */
+ /*
+ public int[] quantizeBlockExtreme(double inputData[][], int code)
+ {
+ int outputData[] = new int[NN];
+ int i, j;
+ int index;
+ index = 0;
+ for (i = 0; i < 8; i++) {
+ for (j = 0; j < 8; j++) {
+ outputData[index] = (int)(Math.round(inputData[i][j] / (((int[]) (quantum[code]))[index])));
+ index++;
+ }
+ }
+
+ return outputData;
+ }
+ */
+}
+
+// This class was modified by James R. Weeks on 3/27/98.
+// It now incorporates Huffman table derivation as in the C jpeg library
+// from the IJG, Jpeg-6a.
+
+class Huffman {
+ private int bufferPutBits, bufferPutBuffer;
+ int imageHeight;
+ int imageWidth;
+ private int dc_matrix0[][];
+ private int ac_matrix0[][];
+ private int dc_matrix1[][];
+ private int ac_matrix1[][];
+ private int[][][] dc_matrix;
+ private int[][][] ac_matrix;
+ //private int code;
+ int numOfDCTables;
+ int numOfACTables;
+ final static int[] bitsDCluminance = { 0x00, 0, 1, 5, 1, 1, 1, 1, 1, 1, 0, 0,
+ 0, 0, 0, 0, 0 };
+ final static int[] valDCluminance = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 };
+ final static int[] bitsDCchrominance = { 0x01, 0, 3, 1, 1, 1, 1, 1, 1, 1, 1,
+ 1, 0, 0, 0, 0, 0 };
+ final static int[] valDCchrominance = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 };
+ final static int[] bitsACluminance = { 0x10, 0, 2, 1, 3, 3, 2, 4, 3, 5, 5, 4,
+ 4, 0, 0, 1, 0x7d };
+ final static int[] valACluminance = { 0x01, 0x02, 0x03, 0x00, 0x04, 0x11,
+ 0x05, 0x12, 0x21, 0x31, 0x41, 0x06, 0x13, 0x51, 0x61, 0x07, 0x22, 0x71,
+ 0x14, 0x32, 0x81, 0x91, 0xa1, 0x08, 0x23, 0x42, 0xb1, 0xc1, 0x15, 0x52,
+ 0xd1, 0xf0, 0x24, 0x33, 0x62, 0x72, 0x82, 0x09, 0x0a, 0x16, 0x17, 0x18,
+ 0x19, 0x1a, 0x25, 0x26, 0x27, 0x28, 0x29, 0x2a, 0x34, 0x35, 0x36, 0x37,
+ 0x38, 0x39, 0x3a, 0x43, 0x44, 0x45, 0x46, 0x47, 0x48, 0x49, 0x4a, 0x53,
+ 0x54, 0x55, 0x56, 0x57, 0x58, 0x59, 0x5a, 0x63, 0x64, 0x65, 0x66, 0x67,
+ 0x68, 0x69, 0x6a, 0x73, 0x74, 0x75, 0x76, 0x77, 0x78, 0x79, 0x7a, 0x83,
+ 0x84, 0x85, 0x86, 0x87, 0x88, 0x89, 0x8a, 0x92, 0x93, 0x94, 0x95, 0x96,
+ 0x97, 0x98, 0x99, 0x9a, 0xa2, 0xa3, 0xa4, 0xa5, 0xa6, 0xa7, 0xa8, 0xa9,
+ 0xaa, 0xb2, 0xb3, 0xb4, 0xb5, 0xb6, 0xb7, 0xb8, 0xb9, 0xba, 0xc2, 0xc3,
+ 0xc4, 0xc5, 0xc6, 0xc7, 0xc8, 0xc9, 0xca, 0xd2, 0xd3, 0xd4, 0xd5, 0xd6,
+ 0xd7, 0xd8, 0xd9, 0xda, 0xe1, 0xe2, 0xe3, 0xe4, 0xe5, 0xe6, 0xe7, 0xe8,
+ 0xe9, 0xea, 0xf1, 0xf2, 0xf3, 0xf4, 0xf5, 0xf6, 0xf7, 0xf8, 0xf9, 0xfa };
+ final static int[] bitsACchrominance = { 0x11, 0, 2, 1, 2, 4, 4, 3, 4, 7, 5,
+ 4, 4, 0, 1, 2, 0x77 };
+ final static int[] valACchrominance = { 0x00, 0x01, 0x02, 0x03, 0x11, 0x04,
+ 0x05, 0x21, 0x31, 0x06, 0x12, 0x41, 0x51, 0x07, 0x61, 0x71, 0x13, 0x22,
+ 0x32, 0x81, 0x08, 0x14, 0x42, 0x91, 0xa1, 0xb1, 0xc1, 0x09, 0x23, 0x33,
+ 0x52, 0xf0, 0x15, 0x62, 0x72, 0xd1, 0x0a, 0x16, 0x24, 0x34, 0xe1, 0x25,
+ 0xf1, 0x17, 0x18, 0x19, 0x1a, 0x26, 0x27, 0x28, 0x29, 0x2a, 0x35, 0x36,
+ 0x37, 0x38, 0x39, 0x3a, 0x43, 0x44, 0x45, 0x46, 0x47, 0x48, 0x49, 0x4a,
+ 0x53, 0x54, 0x55, 0x56, 0x57, 0x58, 0x59, 0x5a, 0x63, 0x64, 0x65, 0x66,
+ 0x67, 0x68, 0x69, 0x6a, 0x73, 0x74, 0x75, 0x76, 0x77, 0x78, 0x79, 0x7a,
+ 0x82, 0x83, 0x84, 0x85, 0x86, 0x87, 0x88, 0x89, 0x8a, 0x92, 0x93, 0x94,
+ 0x95, 0x96, 0x97, 0x98, 0x99, 0x9a, 0xa2, 0xa3, 0xa4, 0xa5, 0xa6, 0xa7,
+ 0xa8, 0xa9, 0xaa, 0xb2, 0xb3, 0xb4, 0xb5, 0xb6, 0xb7, 0xb8, 0xb9, 0xba,
+ 0xc2, 0xc3, 0xc4, 0xc5, 0xc6, 0xc7, 0xc8, 0xc9, 0xca, 0xd2, 0xd3, 0xd4,
+ 0xd5, 0xd6, 0xd7, 0xd8, 0xd9, 0xda, 0xe2, 0xe3, 0xe4, 0xe5, 0xe6, 0xe7,
+ 0xe8, 0xe9, 0xea, 0xf2, 0xf3, 0xf4, 0xf5, 0xf6, 0xf7, 0xf8, 0xf9, 0xfa };
+
+ /*
+ * jpegNaturalOrder[i] is the natural-order position of the i'th element
+ * of zigzag order.
+ */
+ final static int[] jpegNaturalOrder = { 0, 1, 8, 16, 9, 2, 3, 10, 17, 24, 32,
+ 25, 18, 11, 4, 5, 12, 19, 26, 33, 40, 48, 41, 34, 27, 20, 13, 6, 7, 14,
+ 21, 28, 35, 42, 49, 56, 57, 50, 43, 36, 29, 22, 15, 23, 30, 37, 44, 51,
+ 58, 59, 52, 45, 38, 31, 39, 46, 53, 60, 61, 54, 47, 55, 62, 63, };
+
+ Huffman(int width, int height) {
+ initHuf();
+ imageWidth = width;
+ imageHeight = height;
+
+ }
+
+ /**
+ * HuffmanBlockEncoder run length encodes and Huffman encodes the quantized
+ * data.
+ *
+ * @param out
+ * @param zigzag
+ * @param prec
+ * @param dcCode
+ * @param acCode
+ **/
+
+ void HuffmanBlockEncoder(OC out, int zigzag[], int prec,
+ int dcCode, int acCode) {
+ int temp, temp2, nbits, k, r, i;
+
+ numOfDCTables = 2;
+ numOfACTables = 2;
+
+ int[][] matrixDC = dc_matrix[dcCode];
+ int[][] matrixAC = ac_matrix[acCode];
+
+ // The DC portion
+
+ temp = temp2 = zigzag[0] - prec;
+ if (temp < 0) {
+ temp = -temp;
+ temp2--;
+ }
+ nbits = 0;
+ while (temp != 0) {
+ nbits++;
+ temp >>= 1;
+ }
+ // if (nbits > 11) nbits = 11;
+ bufferIt(out, matrixDC[nbits][0], matrixDC[nbits][1]);
+ // The arguments in bufferIt are code and size.
+ if (nbits != 0) {
+ bufferIt(out, temp2, nbits);
+ }
+
+ // The AC portion
+
+ r = 0;
+
+ for (k = 1; k < 64; k++) {
+ if ((temp = zigzag[jpegNaturalOrder[k]]) == 0) {
+ r++;
+ } else {
+ while (r > 15) {
+ bufferIt(out, matrixAC[0xF0][0], matrixAC[0xF0][1]);
+ r -= 16;
+ }
+ temp2 = temp;
+ if (temp < 0) {
+ temp = -temp;
+ temp2--;
+ }
+ nbits = 1;
+ while ((temp >>= 1) != 0) {
+ nbits++;
+ }
+ i = (r << 4) + nbits;
+ bufferIt(out, matrixAC[i][0], matrixAC[i][1]);
+ bufferIt(out, temp2, nbits);
+
+ r = 0;
+ }
+ }
+
+ if (r > 0) {
+ bufferIt(out, matrixAC[0][0], matrixAC[0][1]);
+ }
+
+ }
+
+ // Uses an integer long (32 bits) buffer to store the Huffman encoded bits
+ // and sends them to out by the byte.
+
+ void bufferIt(OC out, int code, int size) {
+ int putBuffer = code;
+ int putBits = bufferPutBits;
+
+ putBuffer &= (1 << size) - 1;
+ putBits += size;
+ putBuffer <<= 24 - putBits;
+ putBuffer |= bufferPutBuffer;
+
+ while (putBits >= 8) {
+ int c = ((putBuffer >> 16) & 0xFF);
+ out.writeByteAsInt(c);
+ if (c == 0xFF) {
+ out.writeByteAsInt(0);
+ }
+ putBuffer <<= 8;
+ putBits -= 8;
+ }
+ bufferPutBuffer = putBuffer;
+ bufferPutBits = putBits;
+
+ }
+
+ void flushBuffer(OC out) {
+ int putBuffer = bufferPutBuffer;
+ int putBits = bufferPutBits;
+ while (putBits >= 8) {
+ int c = ((putBuffer >> 16) & 0xFF);
+ out.writeByteAsInt(c);
+ if (c == 0xFF) {
+ out.writeByteAsInt(0);
+ }
+ putBuffer <<= 8;
+ putBits -= 8;
+ }
+ if (putBits > 0) {
+ int c = ((putBuffer >> 16) & 0xFF);
+ out.writeByteAsInt(c);
+ }
+ }
+
+ /*
+ * Initialisation of the Huffman codes for Luminance and Chrominance.
+ * This code results in the same tables created in the IJG Jpeg-6a
+ * library.
+ */
+
+ private void initHuf() {
+ dc_matrix0 = new int[12][2];
+ dc_matrix1 = new int[12][2];
+ ac_matrix0 = new int[255][2];
+ ac_matrix1 = new int[255][2];
+ dc_matrix = AU.newInt3(2, -1);
+ ac_matrix = AU.newInt3(2, -1);
+ int p, l, i, lastp, si, code;
+ int[] huffsize = new int[257];
+ int[] huffcode = new int[257];
+
+ /*
+ * init of the DC values for the chrominance
+ * [][0] is the code [][1] is the number of bit
+ */
+
+ p = 0;
+ for (l = 1; l <= 16; l++) {
+ // for (i = 1; i <= bitsDCchrominance[l]; i++)
+ for (i = bitsDCchrominance[l]; --i >= 0;) {
+ huffsize[p++] = l; //that's an "el", not a "one"
+ }
+ }
+ huffsize[p] = 0;
+ lastp = p;
+
+ code = 0;
+ si = huffsize[0];
+ p = 0;
+ while (huffsize[p] != 0) {
+ while (huffsize[p] == si) {
+ huffcode[p++] = code;
+ code++;
+ }
+ code <<= 1;
+ si++;
+ }
+
+ for (p = 0; p < lastp; p++) {
+ dc_matrix1[valDCchrominance[p]][0] = huffcode[p];
+ dc_matrix1[valDCchrominance[p]][1] = huffsize[p];
+ }
+
+ /*
+ * Init of the AC huffman code for the chrominance
+ * matrix [][][0] is the code & matrix[][][1] is the number of bit needed
+ */
+
+ p = 0;
+ for (l = 1; l <= 16; l++) {
+ for (i = bitsACchrominance[l]; --i >= 0;)
+ // for (i = 1; i <= bitsACchrominance[l]; i++)
+ {
+ huffsize[p++] = l;
+ }
+ }
+ huffsize[p] = 0;
+ lastp = p;
+
+ code = 0;
+ si = huffsize[0];
+ p = 0;
+ while (huffsize[p] != 0) {
+ while (huffsize[p] == si) {
+ huffcode[p++] = code;
+ code++;
+ }
+ code <<= 1;
+ si++;
+ }
+
+ for (p = 0; p < lastp; p++) {
+ ac_matrix1[valACchrominance[p]][0] = huffcode[p];
+ ac_matrix1[valACchrominance[p]][1] = huffsize[p];
+ }
+
+ /*
+ * init of the DC values for the luminance
+ * [][0] is the code [][1] is the number of bit
+ */
+ p = 0;
+ for (l = 1; l <= 16; l++) {
+ // for (i = 1; i <= bitsDCluminance[l]; i++)
+ for (i = bitsDCluminance[l]; --i >= 0;) {
+ huffsize[p++] = l;
+ }
+ }
+ huffsize[p] = 0;
+ lastp = p;
+
+ code = 0;
+ si = huffsize[0];
+ p = 0;
+ while (huffsize[p] != 0) {
+ while (huffsize[p] == si) {
+ huffcode[p++] = code;
+ code++;
+ }
+ code <<= 1;
+ si++;
+ }
+
+ for (p = 0; p < lastp; p++) {
+ dc_matrix0[valDCluminance[p]][0] = huffcode[p];
+ dc_matrix0[valDCluminance[p]][1] = huffsize[p];
+ }
+
+ /*
+ * Init of the AC huffman code for luminance
+ * matrix [][][0] is the code & matrix[][][1] is the number of bit
+ */
+
+ p = 0;
+ for (l = 1; l <= 16; l++) {
+ // for (i = 1; i <= bitsACluminance[l]; i++)
+ for (i = bitsACluminance[l]; --i >= 0;) {
+ huffsize[p++] = l;
+ }
+ }
+ huffsize[p] = 0;
+ lastp = p;
+
+ code = 0;
+ si = huffsize[0];
+ p = 0;
+ while (huffsize[p] != 0) {
+ while (huffsize[p] == si) {
+ huffcode[p++] = code;
+ code++;
+ }
+ code <<= 1;
+ si++;
+ }
+ for (int q = 0; q < lastp; q++) {
+ ac_matrix0[valACluminance[q]][0] = huffcode[q];
+ ac_matrix0[valACluminance[q]][1] = huffsize[q];
+ }
+
+ dc_matrix[0] = dc_matrix0;
+ dc_matrix[1] = dc_matrix1;
+ ac_matrix[0] = ac_matrix0;
+ ac_matrix[1] = ac_matrix1;
+ }
+
+}
+
+/*
+ * JpegInfo - Given an image, sets default information about it and divides
+ * it into its constituant components, downsizing those that need to be.
+ */
+
+class JpegObj {
+ String comment;
+ int imageHeight;
+ int imageWidth;
+ int blockWidth[];
+ int blockHeight[];
+
+ int precision = 8;
+ int numberOfComponents = 3;
+ float[][][] components;
+ int[] compID = { 1, 2, 3 };
+ int[] hsampFactor = { 1, 1, 1 };
+ int[] vsampFactor = { 1, 1, 1 };
+ int[] qtableNumber = { 0, 1, 1 };
+ int[] dctableNumber = { 0, 1, 1 };
+ int[] actableNumber = { 0, 1, 1 };
+ private boolean[] lastColumnIsDummy = { false, false, false };
+ private boolean[] lastRowIsDummy = { false, false, false };
+ int ss = 0;
+ int se = 63;
+ int ah = 0;
+ int al = 0;
+ private int compWidth[];
+ private int compHeight[];
+ private int maxHsampFactor;
+ private int maxVsampFactor;
+
+ public JpegObj() {
+ components = AU.newFloat3(numberOfComponents, -1);
+ compWidth = new int[numberOfComponents];
+ compHeight = new int[numberOfComponents];
+ blockWidth = new int[numberOfComponents];
+ blockHeight = new int[numberOfComponents];
+ }
+
+ /*
+ * This method creates and fills three arrays, Y, Cb, and Cr using the
+ * input image.
+ */
+
+ void getYCCArray(int[] pixels) {
+ // In order to minimize the chance that grabPixels will throw an exception
+ // it may be necessary to grab some pixels every few scanlines and process
+ // those before going for more. The time expense may be prohibitive.
+ // However, for a situation where memory overhead is a concern, this may be
+ // the only choice.
+ maxHsampFactor = 1;
+ maxVsampFactor = 1;
+ for (int y = 0; y < numberOfComponents; y++) {
+ maxHsampFactor = Math.max(maxHsampFactor, hsampFactor[y]);
+ maxVsampFactor = Math.max(maxVsampFactor, vsampFactor[y]);
+ }
+ for (int y = 0; y < numberOfComponents; y++) {
+ compWidth[y] = (((imageWidth % 8 != 0) ? ((int) Math
+ .ceil(imageWidth / 8.0)) * 8 : imageWidth) / maxHsampFactor)
+ * hsampFactor[y];
+ if (compWidth[y] != ((imageWidth / maxHsampFactor) * hsampFactor[y])) {
+ lastColumnIsDummy[y] = true;
+ }
+ // results in a multiple of 8 for compWidth
+ // this will make the rest of the program fail for the unlikely
+ // event that someone tries to compress an 16 x 16 pixel image
+ // which would of course be worse than pointless
+ blockWidth[y] = (int) Math.ceil(compWidth[y] / 8.0);
+ compHeight[y] = (((imageHeight % 8 != 0) ? ((int) Math
+ .ceil(imageHeight / 8.0)) * 8 : imageHeight) / maxVsampFactor)
+ * vsampFactor[y];
+ if (compHeight[y] != ((imageHeight / maxVsampFactor) * vsampFactor[y])) {
+ lastRowIsDummy[y] = true;
+ }
+ blockHeight[y] = (int) Math.ceil(compHeight[y] / 8.0);
+ }
+ float Y[][] = new float[compHeight[0]][compWidth[0]];
+ float Cr1[][] = new float[compHeight[0]][compWidth[0]];
+ float Cb1[][] = new float[compHeight[0]][compWidth[0]];
+ //float Cb2[][] = new float[compHeight[1]][compWidth[1]];
+ //float Cr2[][] = new float[compHeight[2]][compWidth[2]];
+ for (int pt = 0, y = 0; y < imageHeight; ++y) {
+ for (int x = 0; x < imageWidth; ++x, pt++) {
+ int p = pixels[pt];
+ int r = ((p >> 16) & 0xff);
+ int g = ((p >> 8) & 0xff);
+ int b = (p & 0xff);
+ // The following three lines are a more correct color conversion but
+ // the current conversion technique is sufficient and results in a higher
+ // compression rate.
+ // Y[y][x] = 16 + (float)(0.8588*(0.299 * (float)r + 0.587 * (float)g + 0.114 * (float)b ));
+ // Cb1[y][x] = 128 + (float)(0.8784*(-0.16874 * (float)r - 0.33126 * (float)g + 0.5 * (float)b));
+ // Cr1[y][x] = 128 + (float)(0.8784*(0.5 * (float)r - 0.41869 * (float)g - 0.08131 * (float)b));
+ Y[y][x] = (float) ((0.299 * r + 0.587 * g + 0.114 * b));
+ Cb1[y][x] = 128 + (float) ((-0.16874 * r - 0.33126 * g + 0.5 * b));
+ Cr1[y][x] = 128 + (float) ((0.5 * r - 0.41869 * g - 0.08131 * b));
+ }
+ }
+
+ // Need a way to set the H and V sample factors before allowing downsampling.
+ // For now (04/04/98) downsampling must be hard coded.
+ // Until a better downsampler is implemented, this will not be done.
+ // Downsampling is currently supported. The downsampling method here
+ // is a simple box filter.
+
+ components[0] = Y;
+ // Cb2 = DownSample(Cb1, 1);
+ components[1] = Cb1;
+ // Cr2 = DownSample(Cr1, 2);
+ components[2] = Cr1;
+ }
+ /*
+ float[][] DownSample(float[][] C, int comp)
+ {
+ int inrow, incol;
+ int outrow, outcol;
+ float output[][];
+ int bias;
+ inrow = 0;
+ incol = 0;
+ int cHeight = compHeight[comp];
+ int cWidth = compWidth[comp];
+ output = new float[cHeight][cWidth];
+
+ for (outrow = 0; outrow < cHeight; outrow++) {
+ bias = 1;
+ for (outcol = 0; outcol < cWidth; outcol++) {
+ output[outrow][outcol] = (C[inrow][incol++] + C[inrow++][incol--]
+ + C[inrow][incol++] + C[inrow--][incol++] + bias)/(float)4.0;
+ bias ^= 3;
+ }
+ inrow += 2;
+ incol = 0;
+ }
+ return output;
+ }
+ */
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2009-06-30 18:58:33 -0500 (Tue, 30 Jun 2009) $
+ * $Revision: 11158 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2002-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.img;
+
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.export.PDFCreator;
+
+/**
+ * A relatively primitive PDF generator that just makes a document with an image
+ * in it.
+ *
+ */
+public class PdfEncoder extends ImageEncoder {
+
+ private boolean isLandscape;
+ private PDFCreator pdf;
+ private String comment;
+
+ public PdfEncoder() {
+ // for Class.forName
+ }
+
+ @Override
+ protected void setParams(Map<String, Object> params) {
+ isLandscape = (quality > 1);
+ comment = "Jmol " + (String) params.get("comment");
+ }
+
+ @Override
+ protected void generate() throws Exception {
+ pdf = new PDFCreator();
+ int pageWidth = 8 * 72;
+ int pageHeight = 11 * 72;
+ pdf.setOutputStream(out);
+ pdf.newDocument(pageWidth, pageHeight, isLandscape); // A4 or Letter
+ addMyImage(pageWidth, pageHeight);
+ Map<String, String> ht = new Hashtable<String, String>();
+ if (comment != null)
+ ht.put("Producer", comment);
+ ht.put("Author", "JMol");
+ ht.put("CreationDate", date);
+ pdf.addInfo(ht);
+ pdf.closeDocument();
+ }
+
+
+ /**
+ * centered on the page
+ *
+ * @param pageWidth
+ * @param pageHeight
+ */
+ private void addMyImage(int pageWidth, int pageHeight) {
+ pdf.addImageResource("img1", width, height, pixels, true);
+ int w = (isLandscape ? pageHeight : pageWidth);
+ int h = (isLandscape ? pageWidth : pageHeight);
+ int iw = width;
+ int ih = height;
+ if (iw > 0.9 * w) {
+ ih = (int) (ih * 0.9 * w / iw);
+ iw = (int) (w * 0.9);
+ }
+ if (ih > 0.9 * h) {
+ iw = (int) (iw * 0.9 * h / ih);
+ ih = (int) (h * 0.9);
+ }
+ int x = 0;
+ int y = 0;
+ int x1 = iw;
+ int y1 = ih;
+ if (w > iw) {
+ x = (w - iw) / 2;
+ x1 = iw + x;
+ }
+ if (h > ih) {
+ y = (h - ih) / 2;
+ y1 = ih + y;
+ }
+ pdf.drawImage("img1", x, y, x1, y1, 0, 0, width, height);
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: nicove $
+ * $Date: 2007-03-30 12:26:16 -0500 (Fri, 30 Mar 2007) $
+ * $Revision: 7275 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2002-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.img;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.Map;
+import java.util.zip.Deflater;
+import java.util.zip.DeflaterOutputStream;
+
+
+
+/**
+ *
+ * Modified by Bob Hanson hansonr@stolaf.edu to be a subclass of ImageEncoder
+ * and to use javajs.util.OutputChannel instead of just returning bytes. Also includes:
+ *
+ * -- JavaScript-compatible image processing
+ *
+ * -- transparent background option
+ *
+ * -- more efficient calculation of needs for pngBytes
+ *
+ * -- option to use pre-created PNGJ image data (3/19/14; Jmol 14.1.12)
+ *
+ * -- PNGJ format:
+ *
+ * // IHDR chunk
+ *
+ * // tEXt chunk "Jmol type - <PNG0|PNGJ|PNGT><0000000pt>+<000000len>"
+ *
+ * // tEXt chunk "Software - Jmol <version>"
+ *
+ * // tEXt chunk "Creation Time - <date>"
+ *
+ * // tRNS chunk transparent color, if desired
+ *
+ * // IDAT chunk (image data)
+ *
+ * // IEND chunk
+ *
+ * // [JMOL ZIP FILE APPENDIX]
+ *
+ * Original Comment:
+ *
+ * PngEncoder takes a Java Image object and creates a byte string which can be
+ * saved as a PNG file. The Image is presumed to use the DirectColorModel.
+ *
+ * Thanks to Jay Denny at KeyPoint Software http://www.keypoint.com/ who let me
+ * develop this code on company time.
+ *
+ * You may contact me with (probably very-much-needed) improvements, comments,
+ * and bug fixes at:
+ *
+ * david@catcode.com
+ *
+ * @author J. David Eisenberg
+ * @author http://catcode.com/pngencoder/
+ * @author Christian Ribeaud (christian.ribeaud@genedata.com)
+ * @author Bob Hanson (hansonr@stolaf.edu)
+ *
+ * @version 1.4, 31 March 2000
+ */
+public class PngEncoder extends CRCEncoder {
+
+ /** Constants for filters */
+ public static final int FILTER_NONE = 0;
+ public static final int FILTER_SUB = 1;
+ public static final int FILTER_UP = 2;
+ public static final int FILTER_LAST = 2;
+
+ private static final int PT_FIRST_TAG = 37;
+
+ private boolean encodeAlpha;
+ private int filter = FILTER_NONE;
+ private int bytesPerPixel;
+ private int compressionLevel;
+ private String type;
+ private Integer transparentColor;
+
+ private byte[] appData;
+ private String appPrefix;
+ private String comment;
+ private byte[] bytes;
+
+
+ public PngEncoder() {
+ super();
+ }
+
+ @Override
+ protected void setParams(Map<String, Object> params) {
+ if (quality < 0)
+ quality = (params.containsKey("qualityPNG") ? ((Integer) params
+ .get("qualityPNG")).intValue() : 2);
+ if (quality > 9)
+ quality = 9;
+ encodeAlpha = false;
+ filter = FILTER_NONE;
+ compressionLevel = quality;
+ transparentColor = (Integer) params.get("transparentColor");
+ comment = (String) params.get("comment");
+ type = (params.get("type") + "0000").substring(0, 4);
+ bytes = (byte[]) params.get("pngImgData");
+ appData = (byte[]) params.get("pngAppData");
+ appPrefix = (String) params.get("pngAppPrefix");
+ }
+
+
+
+ @Override
+ protected void generate() throws IOException {
+ if (bytes == null) {
+ if (!pngEncode()) {
+ out.cancel();
+ return;
+ }
+ bytes = getBytes();
+ } else {
+ dataLen = bytes.length;
+ }
+ int len = dataLen;
+ if (appData != null) {
+ setJmolTypeText(appPrefix, bytes, len, appData.length,
+ type);
+ out.write(bytes, 0, len);
+ len = (bytes = appData).length;
+ }
+ out.write(bytes, 0, len);
+ }
+
+
+ /**
+ * Creates an array of bytes that is the PNG equivalent of the current image,
+ * specifying whether to encode alpha or not.
+ *
+ * @return true if successful
+ *
+ */
+ private boolean pngEncode() {
+
+ byte[] pngIdBytes = { -119, 80, 78, 71, 13, 10, 26, 10 };
+
+ writeBytes(pngIdBytes);
+ //hdrPos = bytePos;
+ writeHeader();
+ writeText(getApplicationText(appPrefix, type, 0, 0));
+
+ writeText("Software\0" + comment);
+ writeText("Creation Time\0" + date);
+
+ if (!encodeAlpha && transparentColor != null)
+ writeTransparentColor(transparentColor.intValue());
+ //dataPos = bytePos;
+ return writeImageData();
+ }
+
+ /**
+ * Fill in the Jmol type text area with number of bytes of PNG data and number
+ * of bytes of Jmol state data and fix checksum.
+ *
+ * If we do not do this, then the checksum will be wrong, and Jmol and some
+ * other programs may not be able to read the PNG image.
+ *
+ * This was corrected for Jmol 12.3.30. Between 12.3.7 and 12.3.29, PNG files
+ * created by Jmol have incorrect checksums.
+ *
+ * @param prefix
+ *
+ * @param b
+ * @param nPNG
+ * @param nState
+ * @param type
+ */
+ private static void setJmolTypeText(String prefix, byte[] b, int nPNG, int nState, String type) {
+ String s = "tEXt" + getApplicationText(prefix, type, nPNG, nState);
+ CRCEncoder encoder = new PngEncoder();
+ byte[] test = s.substring(0, 4 + prefix.length()).getBytes();
+ for (int i = test.length; -- i >= 0;)
+ if (b[i + PT_FIRST_TAG] != test[i]) {
+ System.out.println("image is not of the right form; appending data, but not adding tEXt tag.");
+ return;
+ }
+ encoder.setData(b, PT_FIRST_TAG);
+ encoder.writeString(s);
+ encoder.writeCRC();
+ }
+
+ /**
+ * Generate the PNGJ directory identifier:
+ *
+ * xxxxxxxxx\0ttttiiiiiiiii+ddddddddd
+ *
+ * where
+ *
+ * xxxxxxxxx is a unique 9-character software identifier
+ * tttt is a four-byte software-specific type indicator (PNG0, PNGJ, PNGT, etc.)
+ * iiiiiiiii is the file pointer to the start of app data
+ * ddddddddd is the length of the app data
+ *
+ * @param prefix up to 9 characters to allow software to recognize itself
+ * @param type PNGx, where x is J or T for Jmol; original type "PNG" is now "PNG0"
+ * @param nPNG
+ * @param nData
+ * @return
+ */
+ private static String getApplicationText(String prefix, String type,
+ int nPNG, int nData) {
+ String sPNG = "000000000" + nPNG;
+ sPNG = sPNG.substring(sPNG.length() - 9);
+ String sData = "000000000" + nData;
+ sData = sData.substring(sData.length() - 9);
+ if (prefix == null)
+ prefix = "#SwingJS.";
+ if (prefix.length() < 9)
+ prefix = (prefix + ".........");
+ if (prefix.length() > 9)
+ prefix = prefix.substring(0, 9);
+ return prefix + "\0" + type + sPNG + "+" + sData;
+ }
+
+ // /**
+ // * Set the filter to use
+ // *
+ // * @param whichFilter from constant list
+ // */
+ // public void setFilter(int whichFilter) {
+ // this.filter = (whichFilter <= FILTER_LAST ? whichFilter : FILTER_NONE);
+ // }
+
+ // /**
+ // * Retrieve filtering scheme
+ // *
+ // * @return int (see constant list)
+ // */
+ // public int getFilter() {
+ // return filter;
+ // }
+
+ // /**
+ // * Set the compression level to use
+ // *
+ // * @param level 0 through 9
+ // */
+ // public void setCompressionLevel(int level) {
+ // if ((level >= 0) && (level <= 9)) {
+ // this.compressionLevel = level;
+ // }
+ // }
+
+ // /**
+ // * Retrieve compression level
+ // *
+ // * @return int in range 0-9
+ // */
+ // public int getCompressionLevel() {
+ // return compressionLevel;
+ // }
+
+ /**
+ * Write a PNG "IHDR" chunk into the pngBytes array.
+ */
+ private void writeHeader() {
+
+ writeInt4(13);
+ startPos = bytePos;
+ writeString("IHDR");
+ writeInt4(width);
+ writeInt4(height);
+ writeByte(8); // bit depth
+ writeByte(encodeAlpha ? 6 : 2); // color type or direct model
+ writeByte(0); // compression method
+ writeByte(0); // filter method
+ writeByte(0); // no interlace
+ writeCRC();
+ }
+
+ private void writeText(String msg) {
+ writeInt4(msg.length());
+ startPos = bytePos;
+ writeString("tEXt" + msg);
+ writeCRC();
+ }
+
+ /**
+ * Write a PNG "tRNS" chunk into the pngBytes array.
+ *
+ * @param icolor
+ */
+ private void writeTransparentColor(int icolor) {
+
+ writeInt4(6);
+ startPos = bytePos;
+ writeString("tRNS");
+ writeInt2((icolor >> 16) & 0xFF);
+ writeInt2((icolor >> 8) & 0xFF);
+ writeInt2(icolor & 0xFF);
+ writeCRC();
+ }
+
+ private byte[] scanLines; // the scan lines to be compressed
+ private int byteWidth; // width * bytesPerPixel
+
+ //private int hdrPos, dataPos, endPos;
+ //private byte[] priorRow;
+ //private byte[] leftBytes;
+
+
+ /**
+ * Write the image data into the pngBytes array. This will write one or more
+ * PNG "IDAT" chunks. In order to conserve memory, this method grabs as many
+ * rows as will fit into 32K bytes, or the whole image; whichever is less.
+ *
+ *
+ * @return true if no errors; false if error grabbing pixels
+ */
+ private boolean writeImageData() {
+
+ bytesPerPixel = (encodeAlpha ? 4 : 3);
+ byteWidth = width * bytesPerPixel;
+
+ int scanWidth = byteWidth + 1; // the added 1 is for the filter byte
+
+ //boolean doFilter = (filter != FILTER_NONE);
+
+ int rowsLeft = height; // number of rows remaining to write
+ //int startRow = 0; // starting row to process this time through
+ int nRows; // how many rows to grab at a time
+
+ int scanPos; // where we are in the scan lines
+
+ Deflater deflater = new Deflater(compressionLevel);
+ ByteArrayOutputStream outBytes = new ByteArrayOutputStream(1024);
+
+ DeflaterOutputStream compBytes = new DeflaterOutputStream(outBytes,
+ deflater);
+
+ int pt = 0; // overall image byte pointer
+
+ // Jmol note: The entire image has been stored in pixels[] already
+
+ try {
+ while (rowsLeft > 0) {
+ nRows = Math.max(1, Math.min(32767 / scanWidth, rowsLeft));
+ scanLines = new byte[scanWidth * nRows];
+ // if (doFilter)
+ // switch (filter) {
+ // case FILTER_SUB:
+ // leftBytes = new byte[16];
+ // break;
+ // case FILTER_UP:
+ // priorRow = new byte[scanWidth - 1];
+ // break;
+ // }
+ int nPixels = width * nRows;
+ scanPos = 0;
+ //startPos = 1;
+ for (int i = 0; i < nPixels; i++, pt++) {
+ if (i % width == 0) {
+ scanLines[scanPos++] = (byte) filter;
+ //startPos = scanPos;
+ }
+ scanLines[scanPos++] = (byte) ((pixels[pt] >> 16) & 0xff);
+ scanLines[scanPos++] = (byte) ((pixels[pt] >> 8) & 0xff);
+ scanLines[scanPos++] = (byte) ((pixels[pt]) & 0xff);
+ if (encodeAlpha) {
+ scanLines[scanPos++] = (byte) ((pixels[pt] >> 24) & 0xff);
+ }
+ // if (doFilter && i % width == width - 1) {
+ // switch (filter) {
+ // case FILTER_SUB:
+ // filterSub();
+ // break;
+ // case FILTER_UP:
+ // filterUp();
+ // break;
+ // }
+ // }
+ }
+
+ /*
+ * Write these lines to the output area
+ */
+ compBytes.write(scanLines, 0, scanPos);
+
+ //startRow += nRows;
+ rowsLeft -= nRows;
+ }
+ compBytes.close();
+
+ /*
+ * Write the compressed bytes
+ */
+ byte[] compressedLines = outBytes.toByteArray();
+ writeInt4(compressedLines.length);
+ startPos = bytePos;
+ writeString("IDAT");
+ writeBytes(compressedLines);
+ writeCRC();
+ writeEnd();
+ deflater.finish();
+ return true;
+ } catch (IOException e) {
+ System.err.println(e.toString());
+ return false;
+ }
+ }
+
+ /**
+ * Write a PNG "IEND" chunk into the pngBytes array.
+ */
+ private void writeEnd() {
+ writeInt4(0);
+ startPos = bytePos;
+ writeString("IEND");
+ writeCRC();
+ }
+
+ ///**
+ //* Perform "sub" filtering on the given row.
+ //* Uses temporary array leftBytes to store the original values
+ //* of the previous pixels. The array is 16 bytes long, which
+ //* will easily hold two-byte samples plus two-byte alpha.
+ //*
+ //*/
+ //private void filterSub() {
+ // int offset = bytesPerPixel;
+ // int actualStart = startPos + offset;
+ // int leftInsert = offset;
+ // int leftExtract = 0;
+ // //byte current_byte;
+ //
+ // for (int i = actualStart; i < startPos + byteWidth; i++) {
+ // leftBytes[leftInsert] = scanLines[i];
+ // scanLines[i] = (byte) ((scanLines[i] - leftBytes[leftExtract]) % 256);
+ // leftInsert = (leftInsert + 1) % 0x0f;
+ // leftExtract = (leftExtract + 1) % 0x0f;
+ // }
+ //}
+ //
+ ///**
+ //* Perform "up" filtering on the given row. Side effect: refills the prior row
+ //* with current row
+ //*
+ //*/
+ //private void filterUp() {
+ // int nBytes = width * bytesPerPixel;
+ // for (int i = 0; i < nBytes; i++) {
+ // int pt = startPos + i;
+ // byte b = scanLines[pt];
+ // scanLines[pt] = (byte) ((scanLines[pt] - priorRow[i]) % 256);
+ // priorRow[i] = b;
+ // }
+ //}
+
+}
--- /dev/null
+// PpmEncoder - write out an image as a PPM
+//
+// Copyright (C)1996,1998 by Jef Poskanzer <jef@mail.acme.com>. All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
+// ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
+// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+// OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+// HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+// SUCH DAMAGE.
+//
+// Visit the ACME Labs Java page for up-to-date versions of this and other
+// fine Java utilities: http://www.acme.com/java/
+
+package javajs.img;
+
+import java.util.Map;
+
+
+/**
+ * see http://netpbm.sourceforge.net/doc/ppm.html
+ */
+public class PpmEncoder extends ImageEncoder {
+
+ @Override
+ protected void setParams(Map<String, Object> params) {
+ // no params
+ }
+
+ @Override
+ protected void generate() {
+ putString("P6\n");
+ putString(width + " " + height + "\n");
+ putString("255\n");
+ byte[] ppmPixels = new byte[width * 3];
+ for (int pt = 0, row = 0; row < height; ++row) {
+ for (int col = 0, j = 0; col < width; ++col, pt++) {
+ int p = pixels[pt];
+ ppmPixels[j++] = (byte) ((p >> 16) & 0xff);
+ ppmPixels[j++] = (byte) ((p >> 8) & 0xff);
+ ppmPixels[j++] = (byte) (p & 0xff);
+ }
+ out.write(ppmPixels, 0, ppmPixels.length);
+ }
+ }
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+import java.io.Serializable;
+
+import javajs.api.JSONEncodable;
+import javajs.util.T3;
+
+
+
+/**
+ * A 4 element axis angle represented by single precision floating point
+ * x,y,z,angle components. An axis angle is a rotation of angle (radians) about
+ * the vector (x,y,z).
+ *
+ * @version specification 1.1, implementation $Revision: 1.9 $, $Date:
+ * 2006/07/28 17:01:32 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012
+ * for unique constructor and method names
+ * for the optimization of compiled JavaScript using Java2Script.
+ *
+ */
+public class A4 implements JSONEncodable, Serializable {
+
+ /*
+ * I assumed that the length of the axis vector is not significant.
+ */
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+/**
+ * The x coordinate.
+ */
+ public float x;
+
+ /**
+ * The y coordinate.
+ */
+ public float y;
+
+ /**
+ * The z coordinate.
+ */
+ public float z;
+
+ /**
+ * The angle.
+ */
+ public float angle;
+
+ /**
+ * Constructs and initializes a AxisAngle4f to (0,0,1,0).
+ */
+ public A4() {
+ z = 1.0f;
+ }
+
+ /**
+ * Constructs and initializes an AxisAngle4f from the specified x, y, z, and
+ * angle.
+ *
+ * @param x
+ * the x coordinate
+ * @param y
+ * the y coordinate
+ * @param z
+ * the z coordinate
+ * @param angle
+ * the angle.
+ * @return a
+ */
+ public static A4 new4(float x, float y, float z, float angle) {
+ A4 a = new A4();
+ a.set4(x, y, z, angle);
+ return a;
+ }
+
+ /**
+ * Constructs and initializes a AxisAngle4f from the specified AxisAngle4f.
+ *
+ * @param a1
+ * the AxisAngle4f containing the initialization x y z angle data
+ * @return a
+ */
+ public static A4 newAA(A4 a1) {
+ A4 a = new A4();
+ a.set4(a1.x, a1.y, a1.z, a1.angle);
+ return a;
+ }
+
+ /**
+ * Constructs and initializes an AxisAngle4f from the specified axis and
+ * angle.
+ *
+ * @param axis
+ * the axis
+ * @param angle
+ * the angle
+ * @return a
+ */
+ public static A4 newVA(V3 axis, float angle) {
+ A4 a = new A4();
+ a.setVA(axis, angle);
+ return a;
+ }
+
+ /**
+ * Sets the value of this AxisAngle4f to the specified axis and angle.
+ *
+ * @param axis
+ * the axis
+ * @param angle
+ * the angle
+ * @since Java 3D 1.2
+ */
+ public final void setVA(V3 axis, float angle) {
+ x = axis.x;
+ y = axis.y;
+ z = axis.z;
+ this.angle = angle;
+ }
+
+ /**
+ * Sets the value of this axis angle to the specified x,y,z,angle.
+ *
+ * @param x
+ * the x coordinate
+ * @param y
+ * the y coordinate
+ * @param z
+ * the z coordinate
+ * @param angle
+ * the angle
+ */
+ public final void set4(float x, float y, float z, float angle) {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ this.angle = angle;
+ }
+
+ /**
+ * Sets the value of this axis angle to the value of axis angle t1.
+ *
+ * @param a
+ * the axis angle to be copied
+ */
+ public final void setAA(A4 a) {
+ x = a.x;
+ y = a.y;
+ z = a.z;
+ angle = a.angle;
+ }
+
+
+ /**
+ * Sets the value of this axis-angle to the rotational component of the passed
+ * matrix.
+ *
+ * @param m1
+ * the matrix3f
+ */
+ public final void setM(M3 m1) {
+ setFromMat(m1.m00, m1.m01, m1.m02, m1.m10, m1.m11, m1.m12, m1.m20, m1.m21,
+ m1.m22);
+ }
+
+ // helper method
+ private void setFromMat(double m00, double m01, double m02, double m10,
+ double m11, double m12, double m20, double m21,
+ double m22) {
+ // assuming M is normalized.
+
+ double cos = (m00 + m11 + m22 - 1.0) * 0.5;
+ x = (float) (m21 - m12);
+ y = (float) (m02 - m20);
+ z = (float) (m10 - m01);
+ double sin = 0.5 * Math.sqrt(x * x + y * y + z * z);
+ if (sin == 0 && cos == 1) {
+ x = y = 0;
+ z = 1;
+ angle = 0;
+ } else {
+ angle = (float) Math.atan2(sin, cos);
+ }
+
+ // no need to normalize
+ // x /= n;
+ // y /= n;
+ // z /= n;
+ }
+
+ /**
+ * Returns a hash number based on the data values in this object. Two
+ * different AxisAngle4f objects with identical data values (ie, returns true
+ * for equals(AxisAngle4f) ) will return the same hash number. Two vectors
+ * with different data members may return the same hash value, although this
+ * is not likely.
+ */
+ @Override
+ public int hashCode() {
+ return T3.floatToIntBits(x) ^ T3.floatToIntBits(y)
+ ^ T3.floatToIntBits(z) ^ T3.floatToIntBits(angle);
+ }
+
+ /**
+ * Returns true if the Object o is of type AxisAngle4f and all of the data
+ * members of o1 are equal to the corresponding data members in this
+ * AxisAngle4f.
+ *
+ * @param o
+ * the object with which the comparison is made.
+ * @return T/F
+ */
+ @Override
+ public boolean equals(Object o) {
+ if (!(o instanceof A4))
+ return false;
+ A4 a1 = (A4) o;
+ return x == a1.x && y == a1.y && z == a1.z && angle == a1.angle;
+ }
+
+ /**
+ * Returns a string that contains the values of this AxisAngle4f. The form is
+ * (x,y,z,angle).
+ *
+ * @return the String representation
+ */
+ @Override
+ public String toString() {
+ return "(" + x + ", " + y + ", " + z + ", " + angle + ")";
+ }
+
+ @Override
+ public String toJSON() {
+ return "[" + x + "," + y + "," + z + "," + (float) (angle * 180.0 / Math.PI) + "]";
+ }
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2005-11-10 09:52:44 -0600 (Thu, 10 Nov 2005) $
+ * $Revision: 4255 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.util;
+
+// 4/23/15 BH getComponentType fix
+
+import java.lang.reflect.Array;
+
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.Map;
+
+
+final public class AU {
+
+ /**
+ * Very important that this not be used with Int32Array or Float32Array,
+ * because it is not initialize to all zeros in MSIE 9.
+ *
+ * @param array
+ * @param minimumLength
+ * @return array
+ */
+ public static Object ensureLength(Object array, int minimumLength) {
+ return (array != null && getLength(array) >= minimumLength ? array
+ : arrayCopyObject(array, minimumLength));
+ }
+
+ public static String[] ensureLengthS(String[] array, int minimumLength) {
+ return (array != null && array.length >= minimumLength ? array
+ : arrayCopyS(array, minimumLength));
+ }
+
+ public static float[] ensureLengthA(float[] array, int minimumLength) {
+ return (array != null && array.length >= minimumLength ? array: arrayCopyF(array, minimumLength));
+ }
+
+ public static int[] ensureLengthI(int[] array, int minimumLength) {
+ return (array != null && array.length >= minimumLength ? array : arrayCopyI(array, minimumLength));
+ }
+
+ public static short[] ensureLengthShort(short[] array, int minimumLength) {
+ return (array != null && array.length >= minimumLength ? array : arrayCopyShort(array, minimumLength));
+ }
+
+ public static byte[] ensureLengthByte(byte[] array, int minimumLength) {
+ return (array != null && array.length >= minimumLength ? array : arrayCopyByte(array, minimumLength));
+ }
+
+ /**
+ * Very important that this not be used with Int32Array or Float32Array,
+ * because it is not initialized to all zeros in MSIE 9.
+ *
+ * @param array
+ * @return array
+ */
+ public static Object doubleLength(Object array) {
+ return arrayCopyObject(array, (array == null ? 16 : 2 * getLength(array)));
+ }
+
+ public static String[] doubleLengthS(String[] array) {
+ return arrayCopyS(array, (array == null ? 16 : 2 * array.length));
+ }
+
+ public static float[] doubleLengthF(float[] array) {
+ return arrayCopyF(array, (array == null ? 16 : 2 * array.length));
+ }
+
+ public static int[] doubleLengthI(int[] array) {
+ return arrayCopyI(array, (array == null ? 16 : 2 * array.length));
+ }
+
+ public static short[] doubleLengthShort(short[] array) {
+ return arrayCopyShort(array, (array == null ? 16 : 2 * array.length));
+ }
+
+ public static byte[] doubleLengthByte(byte[] array) {
+ return arrayCopyByte(array, (array == null ? 16 : 2 * array.length));
+ }
+
+ public static boolean[] doubleLengthBool(boolean[] array) {
+ return arrayCopyBool(array, (array == null ? 16 : 2 * array.length));
+ }
+
+ public static Object deleteElements(Object array, int firstElement,
+ int nElements) {
+ if (nElements == 0 || array == null)
+ return array;
+ int oldLength = getLength(array);
+ if (firstElement >= oldLength)
+ return array;
+ int n = oldLength - (firstElement + nElements);
+ if (n < 0)
+ n = 0;
+ Object t = newInstanceO(array, firstElement + n);
+ if (firstElement > 0)
+ System.arraycopy(array, 0, t, 0, firstElement);
+ if (n > 0)
+ System.arraycopy(array, firstElement + nElements, t, firstElement, n);
+ return t;
+ }
+
+ /**
+ * note -- cannot copy if array is null! does not copy if length is unchanged
+ *
+ * @param array
+ * @param newLength
+ * @return array
+ */
+ public static Object arrayCopyObject(Object array, int newLength) {
+ int oldLength = (array == null ? -1 : getLength(array));
+ if (newLength < 0) newLength = oldLength;
+ if (newLength == oldLength)
+ return array;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$ && newLength < oldLength) return Clazz.newArray$(-1, array, 0, newLength);
+ */
+ {}
+ Object t = newInstanceO(array, newLength);
+ if (oldLength > 0)
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ return t;
+
+ }
+
+ /**
+ * Very important that this not be used with Int32Array or Float32Array,
+ * because those need to be initialized to all zeros in MSIE 9, and
+ * MSIE 9 cannot distinguish Int32Array or Float32Array from Array.
+ *
+ * @param array
+ * @param n
+ * @return array
+ */
+ private static Object newInstanceO(Object array, int n) {
+ return Array.newInstance(array.getClass().getComponentType(), n);
+ }
+
+ public static int getLength(Object array) {
+ /**
+ * @j2sNative
+ *
+ * return array.length
+ *
+ */
+ {
+ return Array.getLength(array);
+ }
+ }
+
+ public static String[] arrayCopyS(String[] array, int newLength) {
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$ && newLength < oldLength) return Clazz.newArray$(-1, array, 0, newLength);
+ */
+ {}
+ String[] t = new String[newLength];
+ if (array != null) {
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ }
+ return t;
+ }
+
+ public static int[][] arrayCopyII(int[][] array, int newLength) {
+ int[][] t = newInt2(newLength);
+ if (array != null) {
+ int oldLength = array.length;
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ }
+ return t;
+ }
+
+ public static T3[] arrayCopyPt(T3[] array, int newLength) {
+ if (newLength < 0)
+ newLength = array.length;
+ T3[] t = new T3[newLength];
+ if (array != null) {
+ int oldLength = array.length;
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ }
+ return t;
+ }
+
+ public static float[] arrayCopyF(float[] array, int newLength) {
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$ && newLength < oldLength) return Clazz.newArray$(-1, array, 0, newLength);
+ */
+ {}
+ float[] t = new float[newLength];
+ if (array != null) {
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ }
+ return t;
+ }
+
+ public static int[] arrayCopyI(int[] array, int newLength) {
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$ && newLength < oldLength) return Clazz.newArray$(-1, array, 0, newLength);
+ */
+ {}
+ int[] t = new int[newLength];
+ if (array != null) {
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ }
+ return t;
+ }
+
+ /**
+ * a specialized method that allows copying from a starting point either
+ * to the end or to the middle (color schemes, especially)
+ * @param array
+ * @param i0
+ * @param n
+ * @return array or null
+ */
+ public static int[] arrayCopyRangeI(int[] array, int i0, int n) {
+ if (array == null)
+ return null;
+ int oldLength = array.length;
+ if (n == -1) n = oldLength;
+ if (n == -2) n = oldLength / 2;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$) return Clazz.newArray$(-1, array, i0, n);
+ *
+ */
+ {
+ }
+ n -= i0;
+ int[] t = new int[n];
+ System.arraycopy(array, i0, t, 0, n);
+ return t;
+ }
+
+ public static int[] arrayCopyRangeRevI(int[] array, int i0, int n) {
+ if (array == null)
+ return null;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$) return Clazz.newArray$(-1, array, i0, n).reverse();
+ */
+ {
+ }
+ int[] t = arrayCopyRangeI(array, i0, n);
+ if (n < 0)
+ n = array.length;
+ for (int i = n / 2; --i >= 0;)
+ swapInt(t, i, n - 1 - i);
+ return t;
+ }
+
+ public static short[] arrayCopyShort(short[] array, int newLength) {
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$ && newLength < oldLength) return Clazz.newArray$(-1, array, 0, newLength);
+ */
+ {}
+ short[] t = new short[newLength];
+ if (array != null) {
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ }
+ return t;
+ }
+
+ public static byte[] arrayCopyByte(byte[] array, int newLength) {
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$ && newLength < oldLength) return Clazz.newArray$(-1, array, 0, newLength);
+ */
+ {}
+ byte[] t = new byte[newLength];
+ if (array != null) {
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ }
+ return t;
+ }
+
+ public static boolean[] arrayCopyBool(boolean[] array, int newLength) {
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (Clazz.newArray$ && newLength < oldLength) return Clazz.newArray$(-1, array, 0, newLength);
+ */
+ {}
+ boolean[] t = new boolean[newLength];
+ if (array != null) {
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ : newLength);
+ }
+ return t;
+ }
+
+ public static void swapInt(int[] array, int indexA, int indexB) {
+ int t = array[indexA];
+ array[indexA] = array[indexB];
+ array[indexB] = t;
+ }
+
+ /*
+ public static void swap(short[] array, int indexA, int indexB) {
+ short t = array[indexA];
+ array[indexA] = array[indexB];
+ array[indexB] = t;
+ }
+
+ public static void swap(float[] array, int indexA, int indexB) {
+ float t = array[indexA];
+ array[indexA] = array[indexB];
+ array[indexB] = t;
+ }
+ */
+
+ public static String dumpArray(String msg, float[][] A, int x1, int x2, int y1, int y2) {
+ String s = "dumpArray: " + msg + "\n";
+ for (int x = x1; x <= x2; x++)
+ s += "\t*" + x + "*";
+ for (int y = y2; y >= y1; y--) {
+ s += "\n*" + y + "*";
+ for (int x = x1; x <= x2; x++)
+ s += "\t" + (x < A.length && y < A[x].length ? A[x][y] : Float.NaN);
+ }
+ return s;
+ }
+
+ public static String dumpIntArray(int[] A, int n) {
+ String str = "";
+ for (int i = 0; i < n; i++)
+ str += " " + A[i];
+ return str;
+ }
+
+ public static String sortedItem(Lst<String> v, int n) {
+ if (v.size() == 0)
+ return null;
+ if (v.size() == 1)
+ return v.get(0);
+ String[] keys = v.toArray(new String[v.size()]);
+ Arrays.sort(keys);
+ return keys[n % keys.length];
+ }
+
+ /**
+ * Helper method for creating a List<Tx>[] without warnings.
+ *
+ * @param <type> Type of objects in the list.
+ * @param size Array size.
+ * @return Array of List<type>
+ */
+ @SuppressWarnings("unchecked")
+ public static <type> Lst<type>[] createArrayOfArrayList(int size) {
+ return new Lst[size];
+ }
+
+ /**
+ * Helper method for creating a Map<K, V>[] without warnings.
+ *
+ * @param <K> Type of object for the keys in the map.
+ * @param <V> Type of object for the values in the map.
+ * @param size Array size.
+ * @return Array of Map<K, V>
+ */
+ @SuppressWarnings("unchecked")
+ public static <K, V> Map<K, V>[] createArrayOfHashtable(int size) {
+ return new Hashtable[size];
+ }
+
+ public static void swap(Object[] o, int i, int j) {
+ Object oi = o[i];
+ o[i] = o[j];
+ o[j] = oi;
+ }
+
+ public static float[][] newFloat2(int n) {
+ return new float[n][];
+ }
+
+ public static boolean[][] newBool2(int n) {
+ return new boolean[n][];
+ }
+
+ public static int[][] newInt2(int n) {
+ return new int[n][];
+ }
+
+ public static int[][][] newInt3(int nx, int ny) {
+ return (ny < 0 ? new int[nx][][] : new int[nx][ny][]);
+ }
+
+ public static float[][][] newFloat3(int nx, int ny) {
+ return (ny < 0 ? new float[nx][][] : new float[nx][ny][]);
+ }
+
+ public static int[][][][] newInt4(int n) {
+ return new int[n][][][];
+ }
+
+ public static short[][] newShort2(int n) {
+ return new short[n][];
+ }
+
+ public static byte[][] newByte2(int n) {
+ return new byte[n][];
+ }
+
+ public static double[][] newDouble2(int n) {
+ return new double[n][];
+ }
+
+ /**
+ * remove all keys from a map that start with given root
+ * @param map
+ * @param root
+ * @return number removed
+ */
+ public static int removeMapKeys(Map<String, ?> map, String root) {
+ Lst<String> list = new Lst<String>();
+ for (String key: map.keySet())
+ if (key.startsWith(root))
+ list.addLast(key);
+ for (int i = list.size(); --i >= 0;)
+ map.remove(list.get(i));
+ return list.size();
+ }
+
+ public static boolean isAS(Object x) {
+ return x instanceof String[];
+ }
+
+ public static boolean isASS(Object x) {
+ return x instanceof String[][];
+ }
+
+ public static boolean isAP(Object x) {
+ return x instanceof T3[];
+ }
+
+ public static boolean isAF(Object x) {
+ return x instanceof float[];
+ }
+
+ public static boolean isAFloat(Object x) {
+ return x instanceof Float[];
+ }
+
+ public static boolean isAD(Object x) {
+ return x instanceof double[];
+ }
+
+ public static boolean isADD(Object x) {
+ return x instanceof double[][];
+ }
+
+ public static boolean isAB(Object x) {
+ return x instanceof byte[];
+ }
+
+ public static boolean isAI(Object x) {
+ return x instanceof int[];
+ }
+
+ public static boolean isAII(Object x) {
+ return (x instanceof int[][]);
+ }
+
+ public static boolean isAFF(Object x) {
+ return x instanceof float[][];
+ }
+
+ public static boolean isAFFF(Object x) {
+ return x instanceof float[][][];
+ }
+
+ /**
+ * Ensure that we have signed and not unsigned bytes coming out of any
+ * process, but particularly out of file reading.
+ *
+ * @param b
+ * @return b
+ */
+ public static byte[] ensureSignedBytes(byte[] b) {
+ if (b != null) {
+ /**
+ * @j2sNative
+ *
+ * for (var i = b.length; --i >= 0;) { var j = b[i] &
+ * 0xFF; if (j >= 0x80) j -= 0x100; b[i] = j; }
+ *
+ */
+ {
+ }
+ }
+ return b;
+ }
+
+
+}
--- /dev/null
+package javajs.util;
+
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.net.URLConnection;
+
+import javajs.api.ResettableStream;
+import javajs.api.js.J2SObjectInterface;
+
+/**
+ *
+ * A method to allow a JavaScript Ajax
+ *
+ */
+public class AjaxURLConnection extends URLConnection {
+
+ protected AjaxURLConnection(URL url) {
+ super(url);
+ }
+
+ byte[] bytesOut;
+ String postOut = "";
+
+ /**
+ *
+ * doAjax() is where the synchronous call to AJAX is to happen. or at least
+ * where we wait for the asynchronous call to return. This method should fill
+ * the dataIn field with either a string or byte array, or null if you want to
+ * throw an error.
+ *
+ * url, bytesOut, and postOut are all available for use
+ *
+ * the method is "private", but in JavaScript that can still be overloaded.
+ * Just set something to org.jmol.awtjs.JmolURLConnection.prototype.doAjax
+ *
+ * @return file data as a javajs.util.SB or byte[] depending upon the file
+ * type.
+ *
+ *
+ */
+ @SuppressWarnings("null")
+ private Object doAjax(boolean isBinary) {
+ J2SObjectInterface jmol = null;
+ /**
+ * @j2sNative
+ *
+ * jmol = J2S || Jmol;
+ *
+ */
+ {
+ }
+ return jmol._doAjax(url, postOut, bytesOut, isBinary);
+ }
+
+ @Override
+ public void connect() throws IOException {
+ // not expected to be used.
+ }
+
+ public void outputBytes(byte[] bytes) {
+ // type = "application/octet-stream;";
+ bytesOut = bytes;
+ }
+
+ public void outputString(String post) {
+ postOut = post;
+ // type = "application/x-www-form-urlencoded";
+ }
+
+ @Override
+ public InputStream getInputStream() {
+ BufferedInputStream bis = getAttachedStreamData(url);
+ if (bis != null)
+ return bis;
+ Object o = doAjax(true);
+ return (
+ AU.isAB(o) ? Rdr.getBIS((byte[]) o)
+ : o instanceof SB ? Rdr.getBIS(Rdr.getBytesFromSB((SB) o))
+ : o instanceof String ? Rdr.getBIS(((String) o).getBytes())
+ : bis
+ );
+ }
+ @SuppressWarnings("unused")
+ /**
+ * J2S will attach a BufferedInputStream to any URL that is
+ * retrieved using a ClassLoader. This improves performance by
+ * not going back to the server every time a second time, since
+ * the first time in Java is usually just to see if it exists.
+ *
+ * This stream can be re-used, but it has to be reset. Java for some
+ * reason does not allow a BufferedInputStream to fully reset its
+ * inner streams. We enable that by force-casting the stream as a
+ * javax.io stream and then applying resetStream() to that.
+ *
+ *
+ * @param url
+ * @return
+ */
+ public static BufferedInputStream getAttachedStreamData(URL url) {
+ BufferedInputStream bis = null;
+ /**
+ * @j2sNative
+ *
+ * bis = url._streamData;
+ */
+ {
+ }
+ if (bis != null)
+ ((ResettableStream) (Object) bis).resetStream();
+ return bis;
+ }
+
+ /**
+ * @return javajs.util.SB or byte[], depending upon the file type
+ */
+ public Object getContents() {
+ return doAjax(false);
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.net.URLStreamHandler;
+
+
+
+/**
+ *
+ * A method to allow a JavaScript AJAX adapter to
+ * deliver web content to JSmol. This handler is just a formality.
+ *
+ */
+public class AjaxURLStreamHandler extends URLStreamHandler {
+
+ String protocol;
+
+ public AjaxURLStreamHandler(String protocol) {
+ this.protocol = protocol;
+ }
+
+ @Override
+ protected URLConnection openConnection(URL url) throws IOException {
+ return new AjaxURLConnection(url);
+ }
+
+
+ @Override
+ protected String toExternalForm(URL u) {
+ SB result = new SB();
+ result.append(u.getProtocol());
+ result.append(":");
+ if (u.getAuthority() != null && u.getAuthority().length() > 0) {
+ result.append("//");
+ result.append(u.getAuthority());
+ }
+ if (u.getPath() != null) {
+ result.append(u.getPath());
+ }
+ if (u.getQuery() != null) {
+ result.append("?");
+ result.append(u.getQuery());
+ }
+ if (u.getRef() != null) {
+ result.append("#");
+ result.append(u.getRef());
+ }
+ return result.toString();
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+import java.net.URLStreamHandler;
+import java.net.URLStreamHandlerFactory;
+import java.util.Hashtable;
+import java.util.Map;
+
+
+/**
+ *
+ * For handling URL file IO via AJAX in JavaScript version
+ *
+ */
+
+public class AjaxURLStreamHandlerFactory implements URLStreamHandlerFactory {
+
+ Map<String, AjaxURLStreamHandler> htFactories = new Hashtable<String, AjaxURLStreamHandler>();
+
+ public AjaxURLStreamHandlerFactory() {
+ // for reflection;
+ }
+
+ @Override
+ public URLStreamHandler createURLStreamHandler(String protocol) {
+ AjaxURLStreamHandler fac = htFactories.get(protocol);
+ if (fac == null)
+ htFactories.put(protocol, fac = new AjaxURLStreamHandler(protocol));
+ return (fac.protocol == null ? null : fac);
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+import java.io.IOException;
+
+
+
+
+
+
+/**
+ *
+ * ArrayDataReader subclasses BufferedReader and overrides its
+ * read, readLine, mark, and reset methods so that JmolAdapter
+ * works with String[] arrays without any further adaptation.
+ *
+ */
+
+public class ArrayDataReader extends DataReader {
+ private String[] data;
+ private int pt;
+ private int len;
+
+ public ArrayDataReader() {
+ super();
+ }
+
+ @Override
+ public DataReader setData(Object data) {
+ this.data = (String[]) data;
+ len = this.data.length;
+ return this;
+ }
+
+ @Override
+ public int read(char[] buf, int off, int len) throws IOException {
+ return readBuf(buf, off, len);
+ }
+
+ @Override
+ public String readLine() {
+ return (pt < len ? data[pt++] : null);
+ }
+
+ /**
+ *
+ * @param ptr
+ */
+ public void mark(long ptr) {
+ //ignore ptr.
+ ptMark = pt;
+ }
+
+ @Override
+ public void reset() {
+ pt = ptMark;
+ }
+}
\ No newline at end of file
--- /dev/null
+package javajs.util;
+
+public class BArray {
+ public byte[] data;
+
+ public BArray(byte[] data) {
+ this.data = data;
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (o instanceof BArray) {
+ byte[] d = ((BArray) o).data;
+ if (d.length == data.length){
+ for (int i = 0; i < d.length; i++)
+ if (d[i] != data[i])
+ return false;
+ return true;
+ }
+ }
+ return false;
+ }
+
+ @Override
+ public int hashCode() {
+ return data.hashCode();
+ }
+
+ @Override
+ public String toString() {
+ return new String(data);
+ }
+}
--- /dev/null
+package javajs.util;
+
+/**
+ * byte converter
+ *
+ *
+ * @author Bob Hanson hansonr@stolaf.edu
+ *
+ */
+public class BC {
+
+ public BC() {
+ // unnecessary to instantialize unless subclassed
+ }
+
+ public static float bytesToFloat(byte[] bytes, int j, boolean isBigEndian) throws Exception {
+ return intToFloat(bytesToInt(bytes, j, isBigEndian));
+ }
+
+ public static int bytesToShort(byte[] bytes, int j, boolean isBigEndian) {
+ int n = (isBigEndian ? (bytes[j + 1] & 0xff) | (bytes[j] & 0xff) << 8
+ : (bytes[j++] & 0xff) | (bytes[j++] & 0xff) << 8);
+ return (n > 0x7FFF ? n - 0x10000 : n);
+ }
+
+ public static int bytesToInt(byte[] bytes, int j, boolean isBigEndian) {
+ int n = (isBigEndian ? (bytes[j + 3] & 0xff) | (bytes[j + 2] & 0xff) << 8
+ | (bytes[j + 1] & 0xff) << 16 | (bytes[j] & 0xff) << 24
+ : (bytes[j++] & 0xff) | (bytes[j++] & 0xff) << 8
+ | (bytes[j++] & 0xff) << 16 | (bytes[j++] & 0xff) << 24);
+ /**
+ * @j2sNative
+ *
+ * return (n > 0x7FFFFFFF ? n - 0x100000000 : n);
+ *
+ */
+ {
+ return n;
+ }
+ }
+
+ public static int intToSignedInt(int n) {
+ /**
+ * @j2sNative
+ *
+ * return (n > 0x7FFFFFFF ? n - 0x100000000 : n);
+ *
+ */
+ {
+ return n;
+ }
+ }
+ public static float intToFloat(int x) throws Exception {
+ /**
+ * see http://en.wikipedia.org/wiki/Binary32
+ *
+ * [sign] [8 bits power] [23 bits fraction]
+ * 0x80000000 0x7F800000 0x7FFFFF
+ *
+ * (untested)
+ *
+ * @j2sNative
+ *
+ * if (x == 0) return 0;
+ * var o = javajs.util.BC;
+ * if (o.fracIEEE == null)
+ * o.setFracIEEE();
+ * var m = ((x & 0x7F800000) >> 23);
+ * return ((x & 0x80000000) == 0 ? 1 : -1) * o.shiftIEEE((x & 0x7FFFFF) | 0x800000, m - 149);
+ *
+ */
+ {
+ return Float.intBitsToFloat(x);
+ }
+ }
+
+ /**
+ * see http://en.wikipedia.org/wiki/Binary64
+ *
+ * not concerning ourselves with very small or very large numbers and getting
+ * this exactly right. Just need a float here.
+ *
+ * @param bytes
+ * @param j
+ * @param isBigEndian
+ * @return float
+ */
+ public static float bytesToDoubleToFloat(byte[] bytes, int j, boolean isBigEndian) {
+ {
+ // IEEE754: sign (1 bit), exponent (11 bits), fraction (52 bits).
+ // seeeeeee eeeeffff ffffffff ffffffff ffffffff xxxxxxxx xxxxxxxx xxxxxxxx
+ // b1 b2 b3 b4 b5 ---------float ignores----
+
+ if (fracIEEE == null)
+ setFracIEEE();
+
+ /**
+ * @j2sNative
+ * var o = javajs.util.BC;
+ * var b1, b2, b3, b4, b5;
+ *
+ * if (isBigEndian) {
+ * b1 = bytes[j] & 0xFF;
+ * b2 = bytes[j + 1] & 0xFF;
+ * b3 = bytes[j + 2] & 0xFF;
+ * b4 = bytes[j + 3] & 0xFF;
+ * b5 = bytes[j + 4] & 0xFF;
+ * } else {
+ * b1 = bytes[j + 7] & 0xFF;
+ * b2 = bytes[j + 6] & 0xFF;
+ * b3 = bytes[j + 5] & 0xFF;
+ * b4 = bytes[j + 4] & 0xFF;
+ * b5 = bytes[j + 3] & 0xFF;
+ * }
+ * var s = ((b1 & 0x80) == 0 ? 1 : -1);
+ * var e = (((b1 & 0x7F) << 4) | (b2 >> 4)) - 1026;
+ * b2 = (b2 & 0xF) | 0x10;
+ * return s * (o.shiftIEEE(b2, e) + o.shiftIEEE(b3, e - 8) + o.shiftIEEE(b4, e - 16)
+ * + o.shiftIEEE(b5, e - 24));
+ */
+ {
+ double d;
+
+ if (isBigEndian)
+ d = Double.longBitsToDouble((((long) bytes[j]) & 0xff) << 56
+ | (((long) bytes[j + 1]) & 0xff) << 48
+ | (((long) bytes[j + 2]) & 0xff) << 40
+ | (((long) bytes[j + 3]) & 0xff) << 32
+ | (((long) bytes[j + 4]) & 0xff) << 24
+ | (((long) bytes[j + 5]) & 0xff) << 16
+ | (((long) bytes[j + 6]) & 0xff) << 8
+ | (((long) bytes[7]) & 0xff));
+ else
+ d = Double.longBitsToDouble((((long) bytes[j + 7]) & 0xff) << 56
+ | (((long) bytes[j + 6]) & 0xff) << 48
+ | (((long) bytes[j + 5]) & 0xff) << 40
+ | (((long) bytes[j + 4]) & 0xff) << 32
+ | (((long) bytes[j + 3]) & 0xff) << 24
+ | (((long) bytes[j + 2]) & 0xff) << 16
+ | (((long) bytes[j + 1]) & 0xff) << 8
+ | (((long) bytes[j]) & 0xff));
+ return (float) d;
+ }
+
+ }
+ }
+
+ private static float[] fracIEEE;
+
+ private static void setFracIEEE() {
+ fracIEEE = new float[270];
+ for (int i = 0; i < 270; i++)
+ fracIEEE[i] = (float) Math.pow(2, i - 141);
+ // System.out.println(fracIEEE[0] + " " + Parser.FLOAT_MIN_SAFE);
+ // System.out.println(fracIEEE[269] + " " + Float.MAX_VALUE);
+ }
+
+ /**
+ * only concerned about reasonable float values here -- private but not designated; called by JavaScript
+ *
+ * @param f
+ * @param i
+ * @return f * 2^i
+ */
+ static double shiftIEEE(double f, int i) {
+ if (f == 0 || i < -140)
+ return 0;
+ if (i > 128)
+ return Float.MAX_VALUE;
+ return f * fracIEEE[i + 140];
+ }
+
+// static {
+// setFracIEEE();
+// for (int i = -50; i < 50; i++) {
+// float f = i * (float) (Math.random() * Math.pow(2, Math.random() * 100 - 50));
+// int x = Float.floatToIntBits(f);
+// int m = ((x & 0x7F800000) >> 23);
+// float f1 = (float) (f == 0 ? 0 : ((x & 0x80000000) == 0 ? 1 : -1) * shiftIEEE((x & 0x7FFFFF) | 0x800000, m - 149));
+// System.out.println(f + " " + f1);
+// }
+// System.out.println("binarydo");
+// }
+
+
+
+}
--- /dev/null
+/*
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright 1995-2007 Sun Microsystems, Inc. All Rights Reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation. Sun designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Sun in the LICENSE file that accompanied this code.
+ *
+ * This code 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
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Sun Microsystems, Inc., 4150 Network Circle, Santa Clara,
+ * CA 95054 USA or visit www.sun.com if you need additional information or
+ * have any questions.
+ */
+
+package javajs.util;
+
+import javajs.api.JSONEncodable;
+
+
+
+/**
+ *
+ * a fast 32-bit BitSet optimized for Java2Script -- about 25 times faster than
+ * java.util.BitSet
+ *
+ * @author Bob Hanson hansonr@stolaf.edu
+ *
+ * Additions by Bob Hanson to allow for JavaScript mix of int/long Note
+ * that Firefox (Sept 2012) does not really treat "Int32Array" as such,
+ * because any element can be pushed into being a 64-bit number, which
+ * really isn't because the last 8 bits are not usable.
+ *
+ * This class implements a vector of bits that grows as needed. Each
+ * component of the bit set has a {@code boolean} value. The bits of a
+ * {@code BitSet} are indexed by nonnegative integers. Individual
+ * indexed bits can be examined, set, or cleared. One {@code BitSet} may
+ * be used to modify the contents of another {@code BitSet} through
+ * logical AND, logical inclusive OR, and logical exclusive OR
+ * operations.
+ *
+ * <p>
+ * By default, all bits in the set initially have the value {@code
+ * false}.
+ *
+ * <p>
+ * Every bit set has a current size, which is the number of bits of
+ * space currently in use by the bit set. Note that the size is related
+ * to the implementation of a bit set, so it may change with
+ * implementation. The length of a bit set relates to logical length of
+ * a bit set and is defined independently of implementation.
+ *
+ * <p>
+ * Unless otherwise noted, passing a null parameter to any of the
+ * methods in a {@code BitSet} will result in a {@code
+ * NullPointerException}.
+ *
+ * <p>
+ * A {@code BitSet} is not safe for multithreaded use without external
+ * synchronization.
+ *
+ * @author Arthur van Hoff
+ * @author Michael McCloskey
+ * @author Martin Buchholz
+ * @since JDK1.0
+ */
+public class BS implements Cloneable, JSONEncodable {
+ /*
+ * BitSets are packed into arrays of "wrangeords."
+ *
+ * An int, which consists of 32 bits, requiring 5 address bits, is used for
+ * the JavaScript port.
+ */
+ private final static int ADDRESS_BITS_PER_WORD = 5;
+ private final static int BITS_PER_WORD = 1 << ADDRESS_BITS_PER_WORD;
+ protected final static int BIT_INDEX_MASK = BITS_PER_WORD - 1;
+
+ /* Used to shift left or right for a partial word mask */
+ protected static final int WORD_MASK = 0xffffffff;
+
+
+ /**
+ * The internal field corresponding to the serialField "bits".
+ */
+ protected int[] words;
+
+ /**
+ * The number of words in the logical size of this BitSet.
+ */
+ protected transient int wordsInUse = 0;
+
+ /**
+ * Whether the size of "words" is user-specified. If so, we assume the user
+ * knows what he's doing and try harder to preserve it.
+ */
+ private transient boolean sizeIsSticky = false;
+
+ /* use serialVersionUID from JDK 1.0.2 for interoperability */
+ //private static final long serialVersionUID = 7997698588986878753L;
+
+ /**
+ * Given a bit index, return word index containing it.
+ * @param bitIndex
+ * @return b
+ */
+ protected static int wordIndex(int bitIndex) {
+ return bitIndex >> ADDRESS_BITS_PER_WORD;
+ }
+
+ /**
+ * Sets the field wordsInUse to the logical size in words of the bit set.
+ * WARNING:This method assumes that the number of words actually in use is
+ * less than or equal to the current value of wordsInUse!
+ */
+ protected void recalculateWordsInUse() {
+ // Traverse the bitset until a used word is found
+ int i;
+ for (i = wordsInUse - 1; i >= 0; i--)
+ if (words[i] != 0)
+ break;
+
+ wordsInUse = i + 1; // The new logical size
+ }
+
+ /**
+ * Creates a new bit set. All bits are initially {@code false}.
+ */
+ public BS() {
+ initWords(BITS_PER_WORD);
+ sizeIsSticky = false;
+ }
+
+ /**
+ * Creates a bit set whose initial size is large enough to explicitly
+ * represent bits with indices in the range {@code 0} through {@code nbits-1}.
+ * All bits are initially {@code false}.
+ *
+ * @param nbits
+ * the initial size of the bit set
+ * @return bs
+ * @throws NegativeArraySizeException
+ * if the specified initial size is negative
+ */
+ public static BS newN(int nbits) {
+ BS bs = new BS();
+ bs.init(nbits);
+ return bs;
+ }
+
+ protected void init(int nbits) {
+ // nbits can't be negative; size 0 is OK
+ if (nbits < 0)
+ throw new NegativeArraySizeException("nbits < 0: " + nbits);
+ initWords(nbits);
+ sizeIsSticky = true;
+ }
+
+ private void initWords(int nbits) {
+ words = new int[wordIndex(nbits - 1) + 1];
+ }
+
+ /**
+ * Ensures that the BitSet can hold enough words.
+ *
+ * @param wordsRequired
+ * the minimum acceptable number of words.
+ */
+ private void ensureCapacity(int wordsRequired) {
+ if (words.length < wordsRequired) {
+ // Allocate larger of doubled size or required size
+ int request = Math.max(2 * words.length, wordsRequired);
+ setLength(request);
+ sizeIsSticky = false;
+ }
+ }
+
+ /**
+ * Ensures that the BitSet can accommodate a given wordIndex, temporarily
+ * violating the invariants. The caller must restore the invariants before
+ * returning to the user, possibly using recalculateWordsInUse().
+ *
+ * @param wordIndex
+ * the index to be accommodated.
+ */
+ protected void expandTo(int wordIndex) {
+ int wordsRequired = wordIndex + 1;
+ if (wordsInUse < wordsRequired) {
+ ensureCapacity(wordsRequired);
+ wordsInUse = wordsRequired;
+ }
+ }
+
+
+ /**
+ * Sets the bit at the specified index to {@code true}.
+ *
+ * @param bitIndex
+ * a bit index
+ * @throws IndexOutOfBoundsException
+ * if the specified index is negative
+ * @since JDK1.0
+ */
+ public void set(int bitIndex) {
+ if (bitIndex < 0)
+ throw new IndexOutOfBoundsException("bitIndex < 0: " + bitIndex);
+
+ int wordIndex = wordIndex(bitIndex);
+ expandTo(wordIndex);
+
+ words[wordIndex] |= (1 << bitIndex); // Restores invariants
+
+ }
+
+ /**
+ * Sets the bit at the specified index to the specified value.
+ *
+ * @param bitIndex
+ * a bit index
+ * @param value
+ * a boolean value to set
+ * @throws IndexOutOfBoundsException
+ * if the specified index is negative
+ * @since 1.4
+ */
+ public void setBitTo(int bitIndex, boolean value) {
+ if (value)
+ set(bitIndex);
+ else
+ clear(bitIndex);
+ }
+
+ /**
+ * Sets the bits from the specified {@code fromIndex} (inclusive) to the
+ * specified {@code toIndex} (exclusive) to {@code true}.
+ *
+ * @param fromIndex
+ * index of the first bit to be set
+ * @param toIndex
+ * index after the last bit to be set
+ * @throws IndexOutOfBoundsException
+ * if {@code fromIndex} is negative, or {@code toIndex} is negative,
+ * or {@code fromIndex} is larger than {@code toIndex}
+ * @since 1.4
+ */
+ public void setBits(int fromIndex, int toIndex) {
+
+ if (fromIndex == toIndex)
+ return;
+
+ // Increase capacity if necessary
+ int startWordIndex = wordIndex(fromIndex);
+ int endWordIndex = wordIndex(toIndex - 1);
+ expandTo(endWordIndex);
+
+ int firstWordMask = WORD_MASK << fromIndex;
+ int lastWordMask = WORD_MASK >>> -toIndex;
+ if (startWordIndex == endWordIndex) {
+ // Case 1: One word
+ words[startWordIndex] |= (firstWordMask & lastWordMask);
+ } else {
+ // Case 2: Multiple words
+ // Handle first word
+ words[startWordIndex] |= firstWordMask;
+
+ // Handle intermediate words, if any
+ for (int i = startWordIndex + 1; i < endWordIndex; i++)
+ words[i] = WORD_MASK;
+
+ // Handle last word (restores invariants)
+ words[endWordIndex] |= lastWordMask;
+ }
+ }
+
+ /**
+ * Sets the bit specified by the index to {@code false}.
+ *
+ * @param bitIndex
+ * the index of the bit to be cleared
+ * @throws IndexOutOfBoundsException
+ * if the specified index is negative
+ * @since JDK1.0
+ */
+ public void clear(int bitIndex) {
+ if (bitIndex < 0)
+ throw new IndexOutOfBoundsException("bitIndex < 0: " + bitIndex);
+
+ int wordIndex = wordIndex(bitIndex);
+ if (wordIndex >= wordsInUse)
+ return;
+
+ words[wordIndex] &= ~(1 << bitIndex);
+
+ recalculateWordsInUse();
+ }
+
+ /**
+ * Sets the bits from the specified {@code fromIndex} (inclusive) to the
+ * specified {@code toIndex} (exclusive) to {@code false}.
+ *
+ * @param fromIndex
+ * index of the first bit to be cleared
+ * @param toIndex
+ * index after the last bit to be cleared
+ * @throws IndexOutOfBoundsException
+ * if {@code fromIndex} is negative, or {@code toIndex} is negative,
+ * or {@code fromIndex} is larger than {@code toIndex}
+ * @since 1.4
+ */
+ public void clearBits(int fromIndex, int toIndex) {
+ if (fromIndex == toIndex)
+ return;
+
+ int startWordIndex = wordIndex(fromIndex);
+ if (startWordIndex >= wordsInUse)
+ return;
+
+ int endWordIndex = wordIndex(toIndex - 1);
+ if (endWordIndex >= wordsInUse) {
+ toIndex = length();
+ endWordIndex = wordsInUse - 1;
+ }
+
+ int firstWordMask = WORD_MASK << fromIndex;
+ int lastWordMask = WORD_MASK >>> -toIndex;
+ if (startWordIndex == endWordIndex) {
+ // Case 1: One word
+ words[startWordIndex] &= ~(firstWordMask & lastWordMask);
+ } else {
+ // Case 2: Multiple words
+ // Handle first word
+ words[startWordIndex] &= ~firstWordMask;
+
+ // Handle intermediate words, if any
+ for (int i = startWordIndex + 1; i < endWordIndex; i++)
+ words[i] = 0;
+
+ // Handle last word
+ words[endWordIndex] &= ~lastWordMask;
+ }
+
+ recalculateWordsInUse();
+ }
+
+ /**
+ * Sets all of the bits in this BitSet to {@code false}.
+ *
+ * @since 1.4
+ */
+ public void clearAll() {
+ while (wordsInUse > 0)
+ words[--wordsInUse] = 0;
+ }
+
+ /**
+ * Returns the value of the bit with the specified index. The value is {@code
+ * true} if the bit with the index {@code bitIndex} is currently set in this
+ * {@code BitSet}; otherwise, the result is {@code false}.
+ *
+ * @param bitIndex
+ * the bit index
+ * @return the value of the bit with the specified index
+ * @throws IndexOutOfBoundsException
+ * if the specified index is negative
+ */
+ public boolean get(int bitIndex) {
+ if (bitIndex < 0)
+ throw new IndexOutOfBoundsException("bitIndex < 0: " + bitIndex);
+
+ int wordIndex = wordIndex(bitIndex);
+ return (wordIndex < wordsInUse)
+ && ((words[wordIndex] & (1 << bitIndex)) != 0);
+ }
+
+ /**
+ * Returns the index of the first bit that is set to {@code true} that occurs
+ * on or after the specified starting index. If no such bit exists then
+ * {@code -1} is returned.
+ *
+ * <p>
+ * To iterate over the {@code true} bits in a {@code BitSet}, use the
+ * following loop:
+ *
+ * <pre>
+ * @code
+ * for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i+1)) {
+ * // operate on index i here
+ * }}
+ * </pre>
+ *
+ * @param fromIndex
+ * the index to start checking from (inclusive)
+ * @return the index of the next set bit, or {@code -1} if there is no such
+ * bit
+ * @throws IndexOutOfBoundsException
+ * if the specified index is negative
+ * @since 1.4
+ */
+ public int nextSetBit(int fromIndex) {
+ if (fromIndex < 0)
+ throw new IndexOutOfBoundsException("fromIndex < 0: " + fromIndex);
+
+ int u = wordIndex(fromIndex);
+ if (u >= wordsInUse)
+ return -1;
+
+ int word = words[u] & (WORD_MASK << fromIndex);
+
+ while (true) {
+ if (word != 0)
+ return (u * BITS_PER_WORD) + Integer.numberOfTrailingZeros(word);
+ if (++u == wordsInUse)
+ return -1;
+ word = words[u];
+ }
+ }
+
+ /**
+ * Returns the index of the first bit that is set to {@code false} that occurs
+ * on or after the specified starting index.
+ *
+ * @param fromIndex
+ * the index to start checking from (inclusive)
+ * @return the index of the next clear bit
+ * @throws IndexOutOfBoundsException
+ * if the specified index is negative
+ * @since 1.4
+ */
+ public int nextClearBit(int fromIndex) {
+ // Neither spec nor implementation handle bitsets of maximal length.
+ // See 4816253.
+ if (fromIndex < 0)
+ throw new IndexOutOfBoundsException("fromIndex < 0: " + fromIndex);
+
+ int u = wordIndex(fromIndex);
+ if (u >= wordsInUse)
+ return fromIndex;
+
+ int word = ~words[u] & (WORD_MASK << fromIndex);
+
+ while (true) {
+ if (word != 0)
+ return (u * BITS_PER_WORD) + Integer.numberOfTrailingZeros(word);
+ if (++u == wordsInUse)
+ return wordsInUse * BITS_PER_WORD;
+ word = ~words[u];
+ }
+ }
+
+ /**
+ * Returns the "logical size" of this {@code BitSet}: the index of the highest
+ * set bit in the {@code BitSet} plus one. Returns zero if the {@code BitSet}
+ * contains no set bits.
+ *
+ * @return the logical size of this {@code BitSet}
+ * @since 1.2
+ */
+ public int length() {
+ if (wordsInUse == 0)
+ return 0;
+
+ return BITS_PER_WORD * (wordsInUse - 1)
+ + (BITS_PER_WORD - Integer.numberOfLeadingZeros(words[wordsInUse - 1]));
+ }
+
+ /**
+ * Returns true if this {@code BitSet} contains no bits that are set to
+ * {@code true}.
+ *
+ * @return boolean indicating whether this {@code BitSet} is empty
+ * @since 1.4
+ */
+ public boolean isEmpty() {
+ return wordsInUse == 0;
+ }
+
+ /**
+ * Returns true if the specified {@code BitSet} has any bits set to {@code
+ * true} that are also set to {@code true} in this {@code BitSet}.
+ *
+ * @param set
+ * {@code BitSet} to intersect with
+ * @return boolean indicating whether this {@code BitSet} intersects the
+ * specified {@code BitSet}
+ * @since 1.4
+ */
+ public boolean intersects(BS set) {
+ for (int i = Math.min(wordsInUse, set.wordsInUse) - 1; i >= 0; i--)
+ if ((words[i] & set.words[i]) != 0)
+ return true;
+ return false;
+ }
+
+ /**
+ * Returns the number of bits set to {@code true} in this {@code BitSet}.
+ *
+ * @return the number of bits set to {@code true} in this {@code BitSet}
+ * @since 1.4
+ */
+ public int cardinality() {
+ int sum = 0;
+ for (int i = 0; i < wordsInUse; i++)
+ sum += Integer.bitCount(words[i]);
+ return sum;
+ }
+
+ /**
+ * Performs a logical <b>AND</b> of this target bit set with the argument bit
+ * set. This bit set is modified so that each bit in it has the value {@code
+ * true} if and only if it both initially had the value {@code true} and the
+ * corresponding bit in the bit set argument also had the value {@code true}.
+ *
+ * @param set
+ * a bit set
+ */
+ public void and(BS set) {
+ if (this == set)
+ return;
+
+ while (wordsInUse > set.wordsInUse)
+ words[--wordsInUse] = 0;
+
+ // Perform logical AND on words in common
+ for (int i = 0; i < wordsInUse; i++)
+ words[i] &= set.words[i];
+
+ recalculateWordsInUse();
+ }
+
+ /**
+ * Performs a logical <b>OR</b> of this bit set with the bit set argument.
+ * This bit set is modified so that a bit in it has the value {@code true} if
+ * and only if it either already had the value {@code true} or the
+ * corresponding bit in the bit set argument has the value {@code true}.
+ *
+ * @param set
+ * a bit set
+ */
+ public void or(BS set) {
+ if (this == set)
+ return;
+
+ int wordsInCommon = Math.min(wordsInUse, set.wordsInUse);
+
+ if (wordsInUse < set.wordsInUse) {
+ ensureCapacity(set.wordsInUse);
+ wordsInUse = set.wordsInUse;
+ }
+
+ // Perform logical OR on words in common
+ for (int i = 0; i < wordsInCommon; i++)
+ words[i] |= set.words[i];
+
+ // Copy any remaining words
+ if (wordsInCommon < set.wordsInUse)
+ System.arraycopy(set.words, wordsInCommon, words, wordsInCommon,
+ wordsInUse - wordsInCommon);
+
+ }
+
+ /**
+ * Performs a logical <b>XOR</b> of this bit set with the bit set argument.
+ * This bit set is modified so that a bit in it has the value {@code true} if
+ * and only if one of the following statements holds:
+ * <ul>
+ * <li>The bit initially has the value {@code true}, and the corresponding bit
+ * in the argument has the value {@code false}.
+ * <li>The bit initially has the value {@code false}, and the corresponding
+ * bit in the argument has the value {@code true}.
+ * </ul>
+ *
+ * @param set
+ * a bit set
+ */
+ public void xor(BS set) {
+ int wordsInCommon = Math.min(wordsInUse, set.wordsInUse);
+
+ if (wordsInUse < set.wordsInUse) {
+ ensureCapacity(set.wordsInUse);
+ wordsInUse = set.wordsInUse;
+ }
+
+ // Perform logical XOR on words in common
+ for (int i = 0; i < wordsInCommon; i++)
+ words[i] ^= set.words[i];
+
+ // Copy any remaining words
+ if (wordsInCommon < set.wordsInUse)
+ System.arraycopy(set.words, wordsInCommon, words, wordsInCommon,
+ set.wordsInUse - wordsInCommon);
+
+ recalculateWordsInUse();
+ }
+
+ /**
+ * Clears all of the bits in this {@code BitSet} whose corresponding bit is
+ * set in the specified {@code BitSet}.
+ *
+ * @param set
+ * the {@code BitSet} with which to mask this {@code BitSet}
+ * @since 1.2
+ */
+ public void andNot(BS set) {
+ // Perform logical (a & !b) on words in common
+ for (int i = Math.min(wordsInUse, set.wordsInUse) - 1; i >= 0; i--)
+ words[i] &= ~set.words[i];
+
+ recalculateWordsInUse();
+ }
+
+ /**
+ * Returns a hash code value for this bit set. The hash code depends only on
+ * which bits have been set within this <code>BitSet</code>. The algorithm
+ * used to compute it may be described as follows.
+ * <p>
+ * Suppose the bits in the <code>BitSet</code> were to be stored in an array
+ * of <code>long</code> integers called, say, <code>words</code>, in such a
+ * manner that bit <code>k</code> is set in the <code>BitSet</code> (for
+ * nonnegative values of <code>k</code>) if and only if the expression
+ *
+ * <pre>
+ * ((k >> 6) < words.length) && ((words[k >> 6] & (1 << (bit & 0x3F))) != 0)
+ * </pre>
+ *
+ * is true. Then the following definition of the <code>hashCode</code> method
+ * would be a correct implementation of the actual algorithm:
+ *
+ * <pre>
+ * public int hashCode() {
+ * long h = 1234;
+ * for (int i = words.length; --i >= 0;) {
+ * h ˆ= words[i] * (i + 1);
+ * }
+ * return (int) ((h >> 32) ˆ h);
+ * }
+ * </pre>
+ *
+ * Note that the hash code values change if the set of bits is altered.
+ * <p>
+ * Overrides the <code>hashCode</code> method of <code>Object</code>.
+ *
+ * @return a hash code value for this bit set.
+ */
+ @Override
+ public int hashCode() {
+ long h = 1234;
+ for (int i = wordsInUse; --i >= 0;)
+ h ^= words[i] * (i + 1);
+
+ return (int) ((h >> 32) ^ h);
+ }
+
+ /**
+ * Returns the number of bits of space actually in use by this {@code BitSet}
+ * to represent bit values. The maximum element in the set is the size - 1st
+ * element.
+ *
+ * @return the number of bits currently in this bit set
+ */
+ public int size() {
+ return words.length * BITS_PER_WORD;
+ }
+
+ /**
+ * Compares this object against the specified object. The result is {@code
+ * true} if and only if the argument is not {@code null} and is a {@code
+ * Bitset} object that has exactly the same set of bits set to {@code true} as
+ * this bit set. That is, for every nonnegative {@code int} index {@code k},
+ *
+ * <pre>
+ * ((BitSet) obj).get(k) == this.get(k)
+ * </pre>
+ *
+ * must be true. The current sizes of the two bit sets are not compared.
+ *
+ * @param obj
+ * the object to compare with
+ * @return {@code true} if the objects are the same; {@code false} otherwise
+ * @see #size()
+ */
+ @Override
+ public boolean equals(Object obj) {
+ if (!(obj instanceof BS))
+ return false;
+ if (this == obj)
+ return true;
+
+ BS set = (BS) obj;
+
+ if (wordsInUse != set.wordsInUse)
+ return false;
+
+ // Check words in use by both BitSets
+ for (int i = 0; i < wordsInUse; i++)
+ if (words[i] != set.words[i])
+ return false;
+
+ return true;
+ }
+
+ /**
+ * Cloning this {@code BitSet} produces a new {@code BitSet} that is equal to
+ * it. The clone of the bit set is another bit set that has exactly the same
+ * bits set to {@code true} as this bit set.
+ *
+ * @return a clone of this bit set
+ * @see #size()
+ */
+ @Override
+ public Object clone() {
+ if (!sizeIsSticky && wordsInUse != words.length)
+ setLength(wordsInUse);
+ return copy(this);
+ }
+
+ /**
+ * Attempts to reduce internal storage used for the bits in this bit set.
+ * Calling this method may, but is not required to, affect the value returned
+ * by a subsequent call to the {@link #size()} method.
+ * @param n
+ */
+ private void setLength(int n) {
+ /**
+ * @j2sNative
+ * if (n == this.words.length) return;
+ * if (n == this.wordsInUse) {
+ * this.words = Clazz.newArray$(-1, this.words, 0, n);
+ * return;
+ * }
+ */
+ {}
+ int[] a = new int[n];
+ System.arraycopy(words, 0, a, 0, wordsInUse);
+ words = a;
+ }
+
+ /**
+ * Returns a string representation of this bit set. For every index for which
+ * this {@code BitSet} contains a bit in the set state, the decimal
+ * representation of that index is included in the result. Such indices are
+ * listed in order from lowest to highest, separated by ", " (a comma and
+ * a space) and surrounded by braces, resulting in the usual mathematical
+ * notation for a set of integers.
+ *
+ * <p>
+ * Example:
+ *
+ * <pre>
+ * BitSet drPepper = new BitSet();
+ * </pre>
+ *
+ * Now {@code drPepper.toString()} returns "{}".
+ * <p>
+ *
+ * <pre>
+ * drPepper.set(2);
+ * </pre>
+ *
+ * Now {@code drPepper.toString()} returns "{2}".
+ * <p>
+ *
+ * <pre>
+ * drPepper.set(4);
+ * drPepper.set(10);
+ * </pre>
+ *
+ * Now {@code drPepper.toString()} returns "{2, 4, 10}".
+ *
+ * @return a string representation of this bit set
+ */
+ @Override
+ public String toString() {
+ return escape(this, '(', ')');
+ }
+
+ private final static int[] emptyBitmap = new int[0];
+
+ /**
+ * fast copy
+ *
+ * @param bitsetToCopy
+ * @return bs
+ */
+ public static BS copy(BS bitsetToCopy) {
+ BS bs;
+ /**
+ * Clazz.clone will copy wordsInUse and sizeIsSticky,
+ * but just a pointer to the words array.
+ *
+ * @j2sNative
+ *
+ * bs = Clazz.clone(bitsetToCopy);
+ *
+ */
+ {
+ bs = new BS();
+ }
+ int wordCount = bitsetToCopy.wordsInUse;
+ if (wordCount == 0) {
+ bs.words = emptyBitmap;
+ } else {
+
+ /**
+ * Clazz.clone will copy wordsInUse and sizeIsSticky,
+ * but just a pointer to the words array.
+ *
+ * @j2sNative
+ *
+ * bs.words = Clazz.newArray(-1, bitsetToCopy.words, 0, bs.wordsInUse = wordCount);
+ *
+ */
+ {
+ bs.words = new int[bs.wordsInUse = wordCount];
+ System.arraycopy(bitsetToCopy.words, 0, bs.words, 0, wordCount);
+ }
+
+ }
+ return bs;
+ }
+
+ /**
+ *
+ * @param max
+ * @return n bits below max
+ */
+ public int cardinalityN(int max) {
+ int n = cardinality();
+ for (int i = length(); --i >= max;)
+ if (get(i))
+ n--;
+ return n;
+ }
+
+ @Override
+ public String toJSON() {
+
+ int numBits = (wordsInUse > 128 ? cardinality() : wordsInUse
+ * BITS_PER_WORD);
+ SB b = SB.newN(6 * numBits + 2);
+ b.appendC('[');
+
+ int i = nextSetBit(0);
+ if (i != -1) {
+ b.appendI(i);
+ for (i = nextSetBit(i + 1); i >= 0; i = nextSetBit(i + 1)) {
+ int endOfRun = nextClearBit(i);
+ do {
+ b.append(", ").appendI(i);
+ } while (++i < endOfRun);
+ }
+ }
+
+ b.appendC(']');
+ return b.toString();
+ }
+
+ public static String escape(BS bs, char chOpen, char chClose) {
+ if (bs == null)
+ return chOpen + "{}" + chClose;
+ SB s = new SB();
+ s.append(chOpen + "{");
+ int imax = bs.length();
+ int iLast = -1;
+ int iFirst = -2;
+ int i = -1;
+ while (++i <= imax) {
+ boolean isSet = bs.get(i);
+ if (i == imax || iLast >= 0 && !isSet) {
+ if (iLast >= 0 && iFirst != iLast)
+ s.append((iFirst == iLast - 1 ? " " : ":") + iLast);
+ if (i == imax)
+ break;
+ iLast = -1;
+ }
+ if (bs.get(i)) {
+ if (iLast < 0) {
+ s.append((iFirst == -2 ? "" : " ") + i);
+ iFirst = i;
+ }
+ iLast = i;
+ }
+ }
+ s.append("}").appendC(chClose);
+ return s.toString();
+ }
+
+ public static BS unescape(String str) {
+ char ch;
+ int len;
+ if (str == null || (len = (str = str.trim()).length()) < 4
+ || str.equalsIgnoreCase("({null})")
+ || (ch = str.charAt(0)) != '(' && ch != '['
+ || str.charAt(len - 1) != (ch == '(' ? ')' : ']')
+ || str.charAt(1) != '{' || str.indexOf('}') != len - 2)
+ return null;
+ len -= 2;
+ for (int i = len; --i >= 2;)
+ if (!PT.isDigit(ch = str.charAt(i)) && ch != ' ' && ch != '\t'
+ && ch != ':')
+ return null;
+ int lastN = len;
+ while (PT.isDigit(str.charAt(--lastN))) {
+ // loop
+ }
+ if (++lastN == len)
+ lastN = 0;
+ else
+ try {
+ lastN = Integer.parseInt(str.substring(lastN, len));
+ } catch (NumberFormatException e) {
+ return null;
+ }
+ BS bs = BS.newN(lastN);
+ lastN = -1;
+ int iPrev = -1;
+ int iThis = -2;
+ for (int i = 2; i <= len; i++) {
+ switch (ch = str.charAt(i)) {
+ case '\t':
+ case ' ':
+ case '}':
+ if (iThis < 0)
+ break;
+ if (iThis < lastN)
+ return null;
+ lastN = iThis;
+ if (iPrev < 0)
+ iPrev = iThis;
+ bs.setBits(iPrev, iThis + 1);
+ iPrev = -1;
+ iThis = -2;
+ break;
+ case ':':
+ iPrev = lastN = iThis;
+ iThis = -2;
+ break;
+ default:
+ if (PT.isDigit(ch)) {
+ if (iThis < 0)
+ iThis = 0;
+ iThis = (iThis * 10) + (ch - 48);
+ }
+ }
+ }
+ return (iPrev >= 0 ? null : bs);
+ }
+
+}
--- /dev/null
+// Version 1.0a
+// Copyright (C) 1998, James R. Weeks and BioElectroMech.
+// Visit BioElectroMech at www.obrador.com. Email James@obrador.com.
+
+// See license.txt for details about the allowed used of this software.
+// This software is based in part on the work of the Independent JPEG Group.
+// See IJGreadme.txt for details about the Independent JPEG Group's license.
+
+// This encoder is inspired by the Java Jpeg encoder by Florian Raemy,
+// studwww.eurecom.fr/~raemy.
+// It borrows a great deal of code and structure from the Independent
+// Jpeg Group's Jpeg 6a library, Copyright Thomas G. Lane.
+// See license.txt for details.
+
+package javajs.util;
+
+
+public class Base64 {
+
+ // 0 1 2 3 4 5 6
+ // 0123456789012345678901234567890123456789012345678901234567890123
+ private static String base64 = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
+ // 41----------------------5A
+ // 61----------------------7A
+ // 30------39
+ // 2B
+ // 2F
+ // alternative "URL-SAFE" 2D and 5F -_
+
+ private static int[] decode64 = new int[] {
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, //0x00-0x0F
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, //0x10-0x1F
+ 0,0,0,0, 0,0,0,0, 0,0,0,62, 0,62,0,63, //0x20-0x2F
+ 52,53,54,55, 56,57,58,59, 60,61,0,0, 0,0,0,0, //0x30-0x3F
+ 0,0,1,2, 3,4,5,6, 7,8,9,10, 11,12,13,14, //0x40-0x4F
+ 15,16,17,18, 19,20,21,22, 23,24,25,0, 0,0,0,63, //0x50-0x5F
+ 0,26,27,28, 29,30,31,32, 33,34,35,36, 37,38,39,40, //0x60-0x6F
+ 41,42,43,44, 45,46,47,48, 49,50,51,0, 0,0,0,0, //0x70-0x7F
+ };
+
+// public static void write(byte[] bytes, OutputChannel out) {
+// SB sb = getBase64(bytes);
+// int len = sb.length();
+// byte[] b = new byte[1];
+// for (int i = 0; i < len; i++) {
+// b[0] = (byte) sb.charAt(i);
+// out.write(b, 0, 1);
+// }
+// }
+
+ public static byte[] getBytes64(byte[] bytes) {
+ return getBase64(bytes).toBytes(0, -1);
+ }
+
+ /**
+ *
+ * @param bytes
+ * @return BASE64-encoded string, without ";base64,"
+ */
+ public static SB getBase64(byte[] bytes) {
+ long nBytes = bytes.length;
+ SB sout = new SB();
+ if (nBytes == 0)
+ return sout;
+ for (int i = 0, nPad = 0; i < nBytes && nPad == 0;) {
+ if (i % 75 == 0 && i != 0)
+ sout.append("\r\n");
+ nPad = (i + 2 == nBytes ? 1 : i + 1 == nBytes ? 2 : 0);
+ int outbytes = ((bytes[i++] << 16) & 0xFF0000)
+ | ((nPad == 2 ? 0 : bytes[i++] << 8) & 0x00FF00)
+ | ((nPad >= 1 ? 0 : (int) bytes[i++]) & 0x0000FF);
+ //System.out.println(Integer.toHexString(outbytes));
+ sout.appendC(base64.charAt((outbytes >> 18) & 0x3F));
+ sout.appendC(base64.charAt((outbytes >> 12) & 0x3F));
+ sout.appendC(nPad == 2 ? '=' : base64.charAt((outbytes >> 6) & 0x3F));
+ sout.appendC(nPad >= 1 ? '=' : base64.charAt(outbytes & 0x3F));
+ }
+ return sout;
+ }
+
+ //Note: Just a simple decoder here. Nothing fancy at all
+ // Because of the 0s in decode64, this is not a VERIFIER
+ // Rather, it may decode even bad Base64-encoded data
+ //
+ // Bob Hanson 4/2007
+
+ public static byte[] decodeBase64(String strBase64) {
+ int nBytes = 0;
+ int ch;
+ int pt0 = strBase64.indexOf(";base64,") + 1;
+ if (pt0 > 0)
+ pt0 += 7;
+ char[] chars64 = strBase64.toCharArray();
+ int len64 = chars64.length;
+ if (len64 == 0)
+ return new byte[0];
+ for (int i = len64; --i >= pt0;)
+ nBytes += ((ch = chars64[i] & 0x7F) == 'A' || decode64[ch] > 0 ? 3 : 0);
+ nBytes = nBytes >> 2;
+ byte[] bytes = new byte[nBytes];
+ int offset = 18;
+ for (int i = pt0, pt = 0, b = 0; i < len64; i++) {
+ if (decode64[ch = chars64[i] & 0x7F] > 0 || ch == 'A' || ch == '=') {
+ b |= decode64[ch] << offset;
+ //System.out.println(chars64[i] + " " + decode64[ch] + " " + offset + " " + Integer.toHexString(b));
+ offset -= 6;
+ if (offset < 0) {
+ bytes[pt++] = (byte) ((b & 0xFF0000) >> 16);
+ if (pt < nBytes)
+ bytes[pt++] = (byte) ((b & 0xFF00) >> 8);
+ if (pt < nBytes)
+ bytes[pt++] = (byte) (b & 0xFF);
+ offset = 18;
+ b = 0;
+ }
+ }
+ }
+ return bytes;
+ }
+}
\ No newline at end of file
--- /dev/null
+/* $RCSfile$
+ * $Date: 2006-03-18 15:59:33 -0600 (Sat, 18 Mar 2006) $
+ * $Revision: 4652 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: hansonr@stolaf.edu
+ *
+ * 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 Public 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 javajs.util;
+
+
+import java.io.BufferedInputStream;
+import java.io.DataInputStream;
+import java.io.IOException;
+import java.util.Map;
+
+import javajs.api.GenericBinaryDocument;
+import javajs.api.GenericOutputChannel;
+
+/* a basic binary file reader (extended by CompoundDocument).
+ *
+ * Note that YOU are responsible for determining whether a file
+ * is bigEndian or littleEndian; the default is bigEndian.
+ *
+ * JavaScript note: readShort() malfunctioned because (short) (xx << 8)
+ * isn't the same as (int) (xx << 8); same problem in java.io.DataStream
+ *
+ *
+ */
+
+public class BinaryDocument extends BC implements GenericBinaryDocument {
+
+ public BinaryDocument() {
+ }
+
+
+ // called by reflection
+
+ protected DataInputStream stream;
+ protected boolean isRandom = false;
+ protected boolean isBigEndian = true;
+ protected BufferedInputStream bis;
+ protected long nBytes;
+ protected GenericOutputChannel out;
+
+
+ @Override
+ public void close() {
+ if (stream != null)
+ try {
+ stream.close();
+ } catch (IOException e) {
+ // ignore
+ }
+ if (out != null)
+ out.closeChannel();
+ }
+
+ @Override
+ public BinaryDocument setStream(BufferedInputStream bis, boolean isBigEndian) {
+ this.bis = bis;
+ if (bis != null) {
+ stream = new DataInputStream(bis);
+ }
+ this.isBigEndian = isBigEndian;
+ return this;
+ }
+
+ @Override
+ public BufferedInputStream getInputStream() {
+ return bis;
+ }
+
+ @Override
+ public void setStreamData(DataInputStream stream, boolean isBigEndian) {
+ if (stream != null)
+ this.stream = stream;
+ this.isBigEndian = isBigEndian;
+ }
+
+ @Override
+ public void setOutputChannel(GenericOutputChannel out) {
+ this.out = out;
+ }
+
+ public void setRandom(boolean TF) {
+ isRandom = TF;
+ //CANNOT be random for web
+ }
+
+ @Override
+ public byte readByte() throws IOException {
+ nBytes++;
+ return ioReadByte();
+ }
+
+ @Override
+ public int readUInt8() throws IOException {
+ nBytes++;
+ int b = stream.readUnsignedByte();
+ if (out != null)
+ out.writeByteAsInt(b);
+ return b;
+ }
+
+ private byte ioReadByte() throws IOException {
+ byte b = stream.readByte();
+ if (out != null)
+ out.writeByteAsInt(b);
+ return b;
+ }
+
+ @Override
+ public byte[] readBytes(int n) throws IOException {
+ byte[] b = new byte[n];
+ readByteArray(b, 0, n);
+ return b;
+ }
+
+ @Override
+ public int readByteArray(byte[] b, int off, int len) throws IOException {
+ int n = ioRead(b, off, len);
+ nBytes += n;
+ return n;
+ }
+
+ private int ioRead(byte[] b, int off, int len) throws IOException {
+ int m = 0;
+ while (len > 0) {
+ int n = stream.read(b, off, len);
+ m += n;
+ if (n > 0 && out != null)
+ out.write(b, off, n);
+ if (n >= len)
+ break;
+ off += n;
+ len -= n;
+ }
+ return m;
+ }
+
+ @Override
+ public String readString(int nChar) throws IOException {
+ byte[] temp = new byte[nChar];
+ int n = readByteArray(temp, 0, nChar);
+ return new String(temp, 0, n, "UTF-8");
+ }
+
+ @Override
+ public short readShort() throws IOException {
+ nBytes += 2;
+ short n = (isBigEndian ? ioReadShort()
+ : (short) ((ioReadByte() & 0xff)
+ | (ioReadByte() & 0xff) << 8));
+ /**
+ * @j2sNative
+ *
+ * return (n > 0x7FFF ? n - 0x10000 : n);
+ */
+ {
+ return n;
+ }
+ }
+
+ private short ioReadShort() throws IOException {
+ short b = stream.readShort();
+ if (out != null)
+ out.writeShort(b);
+ return b;
+ }
+
+
+ @Override
+ public int readIntLE() throws IOException {
+ nBytes += 4;
+ return readLEInt();
+ }
+
+ @Override
+ public int readInt() throws IOException {
+ nBytes += 4;
+ return (isBigEndian ? ioReadInt() : readLEInt());
+ }
+
+ private int ioReadInt() throws IOException {
+ int i = stream.readInt();
+ if (out != null)
+ out.writeInt(i);
+ return i;
+ }
+
+ @Override
+ public int swapBytesI(int n) {
+ return (((n >> 24) & 0xff)
+ | ((n >> 16) & 0xff) << 8
+ | ((n >> 8) & 0xff) << 16
+ | (n & 0xff) << 24);
+ }
+
+ @Override
+ public short swapBytesS(short n) {
+ return (short) ((((n >> 8) & 0xff)
+ | (n & 0xff) << 8));
+ }
+
+
+ @Override
+ public int readUnsignedShort() throws IOException {
+ nBytes += 2;
+ int a = (ioReadByte() & 0xff);
+ int b = (ioReadByte() & 0xff);
+ return (isBigEndian ? (a << 8) + b : (b << 8) + a);
+ }
+
+ @Override
+ public long readLong() throws IOException {
+ nBytes += 8;
+ return (isBigEndian ? ioReadLong()
+ : ((((long) ioReadByte()) & 0xff)
+ | (((long) ioReadByte()) & 0xff) << 8
+ | (((long) ioReadByte()) & 0xff) << 16
+ | (((long) ioReadByte()) & 0xff) << 24
+ | (((long) ioReadByte()) & 0xff) << 32
+ | (((long) ioReadByte()) & 0xff) << 40
+ | (((long) ioReadByte()) & 0xff) << 48
+ | (((long) ioReadByte()) & 0xff) << 54));
+ }
+
+ private long ioReadLong() throws IOException {
+ long b = stream.readLong();
+ if (out != null)
+ out.writeLong(b);
+ return b;
+ }
+
+ private int readLEInt() throws IOException {
+ ioRead(t8, 0, 4);
+ return bytesToInt(t8, 0, false);
+ }
+
+ byte[] t8 = new byte[8];
+
+ @Override
+ public float readFloat() throws Exception {
+ return intToFloat(readInt());
+ }
+
+ @Override
+ public double readDouble() throws IOException {
+ /**
+ *
+ * reading the float equivalent here in JavaScript
+ *
+ * @j2sNative
+ *
+ * this.readByteArray(this.t8, 0, 8);
+ * return this.bytesToDoubleToFloat(this.t8, 0, this.isBigEndian);
+ *
+ */
+ {
+ nBytes += 8;
+ return (isBigEndian ? ioReadDouble() : Double.longBitsToDouble(readLELong()));
+ }
+ }
+
+ private double ioReadDouble() throws IOException {
+ double d = stream.readDouble();
+ if (out != null)
+ out.writeLong(Double.doubleToRawLongBits(d));
+ return d;
+ }
+
+ private long readLELong() throws IOException {
+ return ((((long) ioReadByte()) & 0xff)
+ | (((long) ioReadByte()) & 0xff) << 8
+ | (((long) ioReadByte()) & 0xff) << 16
+ | (((long) ioReadByte()) & 0xff) << 24
+ | (((long) ioReadByte()) & 0xff) << 32
+ | (((long) ioReadByte()) & 0xff) << 40
+ | (((long) ioReadByte()) & 0xff) << 48
+ | (((long) ioReadByte()) & 0xff) << 56);
+ }
+
+ @Override
+ public void seek(long offset) {
+ // slower, but all that is available using the applet
+ try {
+ if (offset == nBytes)
+ return;
+ if (offset < nBytes) {
+ stream.reset();
+ if (out != null && nBytes != 0)
+ out.reset();
+ nBytes = 0;
+ } else {
+ offset -= nBytes;
+ }
+ if (out == null) {
+ stream.skipBytes((int)offset);
+ } else {
+ readByteArray(new byte[(int)offset], 0, (int) offset);
+ }
+ nBytes += offset;
+ } catch (IOException e) {
+ System.out.println(e.toString());
+ }
+ }
+
+ @Override
+ public long getPosition() {
+ return nBytes;
+ }
+
+ @Override
+ public SB getAllDataFiles(String binaryFileList, String firstFile) {
+ return null;
+ }
+
+ @Override
+ public void getAllDataMapped(String replace, String string,
+ Map<String, String> fileData) {
+ }
+
+
+/* random access -- application only:
+ *
+ void seekFile(long offset) {
+ try {
+ file.seek(offset);
+ } catch (IOException e) {
+ System.out.println(e.getMessage());
+ }
+ }
+*/
+}
--- /dev/null
+package javajs.util;
+
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.api.GenericColor;
+
+/**
+ * ColorUtility
+ *
+ */
+
+public class CU {
+
+ public static String toRGBHexString(GenericColor c) {
+ int rgb = c.getRGB();
+ if (rgb == 0)
+ return "000000";
+ String r = "00" + Integer.toHexString((rgb >> 16) & 0xFF);
+ r = r.substring(r.length() - 2);
+ String g = "00" + Integer.toHexString((rgb >> 8) & 0xFF);
+ g = g.substring(g.length() - 2);
+ String b = "00" + Integer.toHexString(rgb & 0xFF);
+ b = b.substring(b.length() - 2);
+ return r + g + b;
+ }
+
+ public static String toCSSString(GenericColor c) {
+ int opacity = c.getOpacity255();
+ if (opacity == 255)
+ return "#" + toRGBHexString(c);
+ int rgb = c.getRGB();
+ return "rgba(" + ((rgb>>16)&0xFF) + "," + ((rgb>>8)&0xff) + "," + (rgb&0xff) + "," + opacity/255f + ")";
+ }
+
+ private final static String[] colorNames = {
+ "black", // 000000
+ "pewhite", // ffffff
+ "pecyan", // 00ffff
+ "pepurple", // d020ff
+ "pegreen", // 00ff00
+ "peblue", // 6060ff
+ "peviolet", // ff80c0
+ "pebrown", // a42028
+ "pepink", // ffd8d8
+ "peyellow", // ffff00
+ "pedarkgreen", // 00c000
+ "peorange", // ffb000
+ "pelightblue", // b0b0ff
+ "pedarkcyan", // 00a0a0
+ "pedarkgray", // 606060
+
+ "aliceblue", // F0F8FF
+ "antiquewhite", // FAEBD7
+ "aqua", // 00FFFF
+ "aquamarine", // 7FFFD4
+ "azure", // F0FFFF
+ "beige", // F5F5DC
+ "bisque", // FFE4C4
+ "blanchedalmond", // FFEBCD
+ "blue", // 0000FF
+ "blueviolet", // 8A2BE2
+ "brown", // A52A2A
+ "burlywood", // DEB887
+ "cadetblue", // 5F9EA0
+ "chartreuse", // 7FFF00
+ "chocolate", // D2691E
+ "coral", // FF7F50
+ "cornflowerblue", // 6495ED
+ "cornsilk", // FFF8DC
+ "crimson", // DC143C
+ "cyan", // 00FFFF
+ "darkblue", // 00008B
+ "darkcyan", // 008B8B
+ "darkgoldenrod", // B8860B
+ "darkgray", // A9A9A9
+ "darkgreen", // 006400
+ "darkkhaki", // BDB76B
+ "darkmagenta", // 8B008B
+ "darkolivegreen", // 556B2F
+ "darkorange", // FF8C00
+ "darkorchid", // 9932CC
+ "darkred", // 8B0000
+ "darksalmon", // E9967A
+ "darkseagreen", // 8FBC8F
+ "darkslateblue", // 483D8B
+ "darkslategray", // 2F4F4F
+ "darkturquoise", // 00CED1
+ "darkviolet", // 9400D3
+ "deeppink", // FF1493
+ "deepskyblue", // 00BFFF
+ "dimgray", // 696969
+ "dodgerblue", // 1E90FF
+ "firebrick", // B22222
+ "floralwhite", // FFFAF0 16775920
+ "forestgreen", // 228B22
+ "fuchsia", // FF00FF
+ "gainsboro", // DCDCDC
+ "ghostwhite", // F8F8FF
+ "gold", // FFD700
+ "goldenrod", // DAA520
+ "gray", // 808080
+ "green", // 008000
+ "greenyellow", // ADFF2F
+ "honeydew", // F0FFF0
+ "hotpink", // FF69B4
+ "indianred", // CD5C5C
+ "indigo", // 4B0082
+ "ivory", // FFFFF0
+ "khaki", // F0E68C
+ "lavender", // E6E6FA
+ "lavenderblush", // FFF0F5
+ "lawngreen", // 7CFC00
+ "lemonchiffon", // FFFACD
+ "lightblue", // ADD8E6
+ "lightcoral", // F08080
+ "lightcyan", // E0FFFF
+ "lightgoldenrodyellow", // FAFAD2
+ "lightgreen", // 90EE90
+ "lightgrey", // D3D3D3
+ "lightgray", // D3D3D3
+ "lightpink", // FFB6C1
+ "lightsalmon", // FFA07A
+ "lightseagreen", // 20B2AA
+ "lightskyblue", // 87CEFA
+ "lightslategray", // 778899
+ "lightsteelblue", // B0C4DE
+ "lightyellow", // FFFFE0
+ "lime", // 00FF00
+ "limegreen", // 32CD32
+ "linen", // FAF0E6
+ "magenta", // FF00FF
+ "maroon", // 800000
+ "mediumaquamarine", // 66CDAA
+ "mediumblue", // 0000CD
+ "mediumorchid", // BA55D3
+ "mediumpurple", // 9370DB
+ "mediumseagreen", // 3CB371
+ "mediumslateblue", // 7B68EE
+ "mediumspringgreen", // 00FA9A
+ "mediumturquoise", // 48D1CC
+ "mediumvioletred", // C71585
+ "midnightblue", // 191970
+ "mintcream", // F5FFFA
+ "mistyrose", // FFE4E1
+ "moccasin", // FFE4B5
+ "navajowhite", // FFDEAD
+ "navy", // 000080
+ "oldlace", // FDF5E6
+ "olive", // 808000
+ "olivedrab", // 6B8E23
+ "orange", // FFA500
+ "orangered", // FF4500
+ "orchid", // DA70D6
+ "palegoldenrod", // EEE8AA
+ "palegreen", // 98FB98
+ "paleturquoise", // AFEEEE
+ "palevioletred", // DB7093
+ "papayawhip", // FFEFD5
+ "peachpuff", // FFDAB9
+ "peru", // CD853F
+ "pink", // FFC0CB
+ "plum", // DDA0DD
+ "powderblue", // B0E0E6
+ "purple", // 800080
+ "red", // FF0000
+ "rosybrown", // BC8F8F
+ "royalblue", // 4169E1
+ "saddlebrown", // 8B4513
+ "salmon", // FA8072
+ "sandybrown", // F4A460
+ "seagreen", // 2E8B57
+ "seashell", // FFF5EE
+ "sienna", // A0522D
+ "silver", // C0C0C0
+ "skyblue", // 87CEEB
+ "slateblue", // 6A5ACD
+ "slategray", // 708090
+ "snow", // FFFAFA 16775930
+ "springgreen", // 00FF7F
+ "steelblue", // 4682B4
+ "tan", // D2B48C
+ "teal", // 008080
+ "thistle", // D8BFD8
+ "tomato", // FF6347
+ "turquoise", // 40E0D0
+ "violet", // EE82EE
+ "wheat", // F5DEB3
+ "white", // FFFFFF 16777215
+ "whitesmoke", // F5F5F5
+ "yellow", // FFFF00
+ "yellowgreen", // 9ACD32
+ // plus a few rasmol names/values
+ "bluetint", // AFD7FF
+ "greenblue", // 2E8B57
+ "greentint", // 98FFB3
+ "grey", // 808080
+ "gray",
+ "pinktint", // FFABBB
+ "redorange", // FF4500
+ "yellowtint", // F6F675
+ };
+
+ private final static int[] colorArgbs = {
+ //#FFFFC3 hover
+ 0xFF000000, // black
+ // plus the PE chain colors
+ 0xFFffffff, // pewhite
+ 0xFF00ffff, // pecyan
+ 0xFFd020ff, // pepurple
+ 0xFF00ff00, // pegreen
+ 0xFF6060ff, // peblue
+ 0xFFff80c0, // peviolet
+ 0xFFa42028, // pebrown
+ 0xFFffd8d8, // pepink
+ 0xFFffff00, // peyellow
+ 0xFF00c000, // pedarkgreen
+ 0xFFffb000, // peorange
+ 0xFFb0b0ff, // pelightblue
+ 0xFF00a0a0, // pedarkcyan
+ 0xFF606060, // pedarkgray
+ // standard JavaScript
+ 0xFFF0F8FF, // aliceblue
+ 0xFFFAEBD7, // antiquewhite
+ 0xFF00FFFF, // aqua
+ 0xFF7FFFD4, // aquamarine
+ 0xFFF0FFFF, // azure
+ 0xFFF5F5DC, // beige
+ 0xFFFFE4C4, // bisque
+ 0xFFFFEBCD, // blanchedalmond
+ 0xFF0000FF, // blue
+ 0xFF8A2BE2, // blueviolet
+ 0xFFA52A2A, // brown
+ 0xFFDEB887, // burlywood
+ 0xFF5F9EA0, // cadetblue
+ 0xFF7FFF00, // chartreuse
+ 0xFFD2691E, // chocolate
+ 0xFFFF7F50, // coral
+ 0xFF6495ED, // cornflowerblue
+ 0xFFFFF8DC, // cornsilk
+ 0xFFDC143C, // crimson
+ 0xFF00FFFF, // cyan
+ 0xFF00008B, // darkblue
+ 0xFF008B8B, // darkcyan
+ 0xFFB8860B, // darkgoldenrod
+ 0xFFA9A9A9, // darkgray
+ 0xFF006400, // darkgreen
+
+ 0xFFBDB76B, // darkkhaki
+ 0xFF8B008B, // darkmagenta
+ 0xFF556B2F, // darkolivegreen
+ 0xFFFF8C00, // darkorange
+ 0xFF9932CC, // darkorchid
+ 0xFF8B0000, // darkred
+ 0xFFE9967A, // darksalmon
+ 0xFF8FBC8F, // darkseagreen
+ 0xFF483D8B, // darkslateblue
+ 0xFF2F4F4F, // darkslategray
+ 0xFF00CED1, // darkturquoise
+ 0xFF9400D3, // darkviolet
+ 0xFFFF1493, // deeppink
+ 0xFF00BFFF, // deepskyblue
+ 0xFF696969, // dimgray
+ 0xFF1E90FF, // dodgerblue
+ 0xFFB22222, // firebrick
+ 0xFFFFFAF0, // floralwhite
+ 0xFF228B22, // forestgreen
+ 0xFFFF00FF, // fuchsia
+ 0xFFDCDCDC, // gainsboro
+ 0xFFF8F8FF, // ghostwhite
+ 0xFFFFD700, // gold
+ 0xFFDAA520, // goldenrod
+ 0xFF808080, // gray
+ 0xFF008000, // green
+ 0xFFADFF2F, // greenyellow
+ 0xFFF0FFF0, // honeydew
+ 0xFFFF69B4, // hotpink
+ 0xFFCD5C5C, // indianred
+ 0xFF4B0082, // indigo
+ 0xFFFFFFF0, // ivory
+ 0xFFF0E68C, // khaki
+ 0xFFE6E6FA, // lavender
+ 0xFFFFF0F5, // lavenderblush
+ 0xFF7CFC00, // lawngreen
+ 0xFFFFFACD, // lemonchiffon
+ 0xFFADD8E6, // lightblue
+ 0xFFF08080, // lightcoral
+ 0xFFE0FFFF, // lightcyan
+ 0xFFFAFAD2, // lightgoldenrodyellow
+ 0xFF90EE90, // lightgreen
+ 0xFFD3D3D3, // lightgrey
+ 0xFFD3D3D3, // lightgray
+ 0xFFFFB6C1, // lightpink
+ 0xFFFFA07A, // lightsalmon
+ 0xFF20B2AA, // lightseagreen
+ 0xFF87CEFA, // lightskyblue
+ 0xFF778899, // lightslategray
+ 0xFFB0C4DE, // lightsteelblue
+ 0xFFFFFFE0, // lightyellow
+ 0xFF00FF00, // lime
+ 0xFF32CD32, // limegreen
+ 0xFFFAF0E6, // linen
+ 0xFFFF00FF, // magenta
+ 0xFF800000, // maroon
+ 0xFF66CDAA, // mediumaquamarine
+ 0xFF0000CD, // mediumblue
+ 0xFFBA55D3, // mediumorchid
+ 0xFF9370DB, // mediumpurple
+ 0xFF3CB371, // mediumseagreen
+ 0xFF7B68EE, // mediumslateblue
+ 0xFF00FA9A, // mediumspringgreen
+ 0xFF48D1CC, // mediumturquoise
+ 0xFFC71585, // mediumvioletred
+ 0xFF191970, // midnightblue
+ 0xFFF5FFFA, // mintcream
+ 0xFFFFE4E1, // mistyrose
+ 0xFFFFE4B5, // moccasin
+ 0xFFFFDEAD, // navajowhite
+ 0xFF000080, // navy
+ 0xFFFDF5E6, // oldlace
+ 0xFF808000, // olive
+ 0xFF6B8E23, // olivedrab
+ 0xFFFFA500, // orange
+ 0xFFFF4500, // orangered
+ 0xFFDA70D6, // orchid
+ 0xFFEEE8AA, // palegoldenrod
+ 0xFF98FB98, // palegreen
+ 0xFFAFEEEE, // paleturquoise
+ 0xFFDB7093, // palevioletred
+ 0xFFFFEFD5, // papayawhip
+ 0xFFFFDAB9, // peachpuff
+ 0xFFCD853F, // peru
+ 0xFFFFC0CB, // pink
+ 0xFFDDA0DD, // plum
+ 0xFFB0E0E6, // powderblue
+ 0xFF800080, // purple
+ 0xFFFF0000, // red
+ 0xFFBC8F8F, // rosybrown
+ 0xFF4169E1, // royalblue
+ 0xFF8B4513, // saddlebrown
+ 0xFFFA8072, // salmon
+ 0xFFF4A460, // sandybrown
+ 0xFF2E8B57, // seagreen
+ 0xFFFFF5EE, // seashell
+ 0xFFA0522D, // sienna
+ 0xFFC0C0C0, // silver
+ 0xFF87CEEB, // skyblue
+ 0xFF6A5ACD, // slateblue
+ 0xFF708090, // slategray
+ 0xFFFFFAFA, // snow
+ 0xFF00FF7F, // springgreen
+ 0xFF4682B4, // steelblue
+ 0xFFD2B48C, // tan
+ 0xFF008080, // teal
+ 0xFFD8BFD8, // thistle
+ 0xFFFF6347, // tomato
+ 0xFF40E0D0, // turquoise
+ 0xFFEE82EE, // violet
+ 0xFFF5DEB3, // wheat
+ 0xFFFFFFFF, // white
+ 0xFFF5F5F5, // whitesmoke
+ 0xFFFFFF00, // yellow
+ 0xFF9ACD32, // yellowgreen
+ // plus a few rasmol names/values
+ 0xFFAFD7FF, // bluetint
+ 0xFF2E8B57, // greenblue
+ 0xFF98FFB3, // greentint
+ 0xFF808080, // grey
+ 0xFF808080, // gray
+ 0xFFFFABBB, // pinktint
+ 0xFFFF4500, // redorange
+ 0xFFF6F675, // yellowtint
+ };
+
+ private static final Map<String, Integer> mapJavaScriptColors = new Hashtable<String, Integer>();
+
+ static {
+ for (int i = colorNames.length; --i >= 0; )
+ mapJavaScriptColors.put(colorNames[i], Integer.valueOf(colorArgbs[i]));
+ }
+
+ /**
+ * accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or
+ * [red,green,blue] or a valid JavaScript color
+ *
+ * @param strColor
+ * @return 0 if invalid or integer color
+ */
+ public static int getArgbFromString(String strColor) {
+ int len = 0;
+ if (strColor == null || (len = strColor.length()) == 0)
+ return 0;
+ strColor = strColor.toLowerCase();
+ if (strColor.charAt(0) == '[' && strColor.charAt(len - 1) == ']') {
+ String check;
+ if (strColor.indexOf(",") >= 0) {
+ String[] tokens = PT.split(strColor.substring(1, strColor
+ .length() - 1), ",");
+ if (tokens.length != 3)
+ return 0;
+ float red = PT.parseFloat(tokens[0]);
+ float grn = PT.parseFloat(tokens[1]);
+ float blu = PT.parseFloat(tokens[2]);
+ return colorTriadToFFRGB(red, grn, blu);
+ }
+ switch (len) {
+ case 9:
+ check = "x";
+ break;
+ case 10:
+ check = "0x";
+ break;
+ default:
+ return 0;
+ }
+ if (strColor.indexOf(check) != 1)
+ return 0;
+ strColor = "#" + strColor.substring(len - 7, len - 1);
+ len = 7;
+ }
+ if (len == 7 && strColor.charAt(0) == '#') {
+ try {
+ return PT.parseIntRadix(strColor.substring(1, 7), 16) | 0xFF000000;
+ } catch (Exception e) {
+ return 0;
+ }
+ }
+ Integer boxedArgb = mapJavaScriptColors.get(strColor);
+ return (boxedArgb == null ? 0 : boxedArgb.intValue());
+ }
+
+ public static int colorTriadToFFRGB(float x, float y, float z) {
+ if (x <= 1 && y <= 1 && z <= 1) {
+ if (x > 0)
+ x = x * 256 - 1;
+ if (y > 0)
+ y = y * 256 - 1;
+ if (z > 0)
+ z = z * 256 - 1;
+ }
+ return rgb((int) x, (int) y, (int) z);
+ }
+
+ public static int rgb(int red, int grn, int blu) {
+ return 0xFF000000 | (red << 16) | (grn << 8) | blu;
+ }
+
+ public final static P3 colorPtFromString(String colorName) {
+ return colorPtFromInt(getArgbFromString(colorName), null);
+ }
+
+ public final static P3 colorPtFromInt(int color, P3 pt) {
+ if (pt == null)
+ pt = new P3();
+ pt.set((color >> 16) & 0xFF, (color >> 8) & 0xFF, color & 0xFF);
+ return pt;
+ }
+
+ public static int colorPtToFFRGB(T3 pt) {
+ return colorTriadToFFRGB(pt.x, pt.y, pt.z);
+ }
+
+ public static void toRGB3f(int c, float[] f) {
+ f[0] = ((c >> 16) & 0xFF) / 255f; // red
+ f[1] = ((c >> 8) & 0xFF) / 255f;
+ f[2] = (c & 0xFF) / 255f;
+ }
+
+ /**
+ * Return a greyscale rgb value 0-FF using NTSC color lightness algorithm
+ *<p>
+ * the alpha component is set to 0xFF. If you want a value in the
+ * range 0-255 then & the result with 0xFF;
+ *
+ * @param rgb the rgb value
+ * @return a grayscale value in the range 0 - 255 decimal
+ */
+ public static int toFFGGGfromRGB(int rgb) {
+ int grey = (((2989 * ((rgb >> 16) & 0xFF)) +
+ (5870 * ((rgb >> 8) & 0xFF)) +
+ (1140 * (rgb & 0xFF)) + 5000) / 10000) & 0xFFFFFF;
+ return rgb(grey, grey, grey);
+ }
+
+
+ /**
+ * Convert RGB values to HSL (hue/saturation/lightness)
+ *
+ * @param rgb
+ * range 255 255 255
+ * @param doRound
+ * set to false when just using this for
+ * for RGB -- HSL -- HSL' -- RGB' conversion
+ *
+ * @return the HSL as P3 range 360 100 100
+ * @author hansonr
+ */
+
+ public static P3 rgbToHSL(P3 rgb, boolean doRound) {
+ // adapted from http://tips4java.wordpress.com/2009/07/05/hsl-color/
+ // see http://en.wikipedia.org/wiki/HSL_color_space
+ float r = rgb.x / 255;
+ float g = rgb.y / 255;
+ float b = rgb.z / 255;
+ float min = Math.min(r, Math.min(g, b));
+ float max = Math.max(r, Math.max(g, b));
+
+ // lightness is just p * 50
+
+ float p = (max + min);
+ float q = (max - min);
+
+ float h = (60 * ((q == 0 ? 0 : max == r ? ((g - b) / q + 6)
+ : max == g ? (b - r) / q + 2 : (r - g) / q + 4))) % 360;
+
+ float s = q / (q == 0 ? 1 : p <= 1 ? p : 2 - p);
+
+ // we round to tenths for HSL so that we can return enough
+ // precision to get back 1-255 in RGB
+ return (doRound ? P3.new3(Math.round(h*10)/10f, Math.round(s * 1000)/10f,
+ Math.round(p * 500)/10f) : P3.new3(h, s * 100, p * 50));
+ }
+
+ /**
+ * Convert HSL (hue/saturation/luninance) values to RGB
+ *
+ * @param hsl in the range 360, 100, 100
+ * @return the RGB as P3 range 0 to 255
+ * @author hansonr
+ */
+ public static P3 hslToRGB(P3 hsl) {
+ // adapted from http://tips4java.wordpress.com/2009/07/05/hsl-color/
+ // see http://en.wikipedia.org/wiki/HSL_color_space
+
+ // highly condensed
+
+ float h = Math.max(0, Math.min(360, hsl.x)) / 60;
+ float s = Math.max(0, Math.min(100, hsl.y)) / 100;
+ float l = Math.max(0, Math.min(100, hsl.z)) / 100;
+
+ float p = l - (l < 0.5 ? l : 1 - l) * s;
+ float q = 2 * (l - p);
+
+ float r = toRGB(p, q, h + 2);
+ float g = toRGB(p, q, h);
+ float b = toRGB(p, q, h - 2);
+ return P3.new3(Math.round(r * 255), Math.round(g * 255), Math.round(b * 255));
+ }
+
+ private static float toRGB(float p, float q, float h) {
+ return ((h = (h + (h < 0 ? 6 : h > 6 ? -6 : 0))) < 1 ? p + q * h
+ : h < 3 ? p + q : h < 4 ? p + q * (4 - h) : p);
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+import java.io.BufferedReader;
+
+import java.util.Hashtable;
+
+import java.util.Map;
+
+import javajs.api.GenericCifDataParser;
+import javajs.api.GenericLineReader;
+
+
+// BH 11/21/16 -- adds support for array grouping [...] - used in 2016-format magCIF files
+
+/**
+*
+* A CIF 1.0 tokenizer class for dealing with quoted strings in CIF files.
+*
+* Subclassed by org.jmol.adapters.readers.cif.Cif2DataParser
+*
+* Greek letters implemented in Jmol 13.3.9 and only for
+* titles and space groups. All other mark ups ignored.
+*
+*<p>
+* regarding the treatment of single quotes vs. primes in
+* cif file, PMR wrote:
+*</p>
+*<p>
+* * There is a formal grammar for CIF
+* (see http://www.iucr.org/iucr-top/cif/index.html)
+* which confirms this. The textual explanation is
+*<p />
+*<p>
+* 14. Matching single or double quote characters (' or ") may
+* be used to bound a string representing a non-simple data value
+* provided the string does not extend over more than one line.
+*<p />
+*<p>
+* 15. Because data values are invariably separated from other
+* tokens in the file by white space, such a quote-delimited
+* character string may contain instances of the character used
+* to delimit the string provided they are not followed by white
+* space. For example, the data item
+*<code>
+* _example 'a dog's life'
+*</code>
+* is legal; the data value is a dog's life.
+*</p>
+*<p>
+* [PMR - the terminating character(s) are quote+whitespace.
+* That would mean that:
+*<code>
+* _example 'Jones' life'
+*</code>
+* would be an error
+*</p>
+*<p>
+* The CIF format was developed in that late 1980's under the aegis of the
+* International Union of Crystallography (I am a consultant to the COMCIFs
+* committee). It was ratified by the Union and there have been several
+* workshops. mmCIF is an extension of CIF which includes a relational
+* structure. The formal publications are:
+*</p>
+*<p>
+* Hall, S. R. (1991). "The STAR File: A New Format for Electronic Data
+* Transfer and Archiving", J. Chem. Inform. Comp. Sci., 31, 326-333.
+* Hall, S. R., Allen, F. H. and Brown, I. D. (1991). "The Crystallographic
+* Information File (CIF): A New Standard Archive File for Crystallography",
+* Acta Cryst., A47, 655-685.
+* Hall, S.R. & Spadaccini, N. (1994). "The STAR File: Detailed
+* Specifications," J. Chem. Info. Comp. Sci., 34, 505-508.
+*</p>
+*/
+
+public class CifDataParser implements GenericCifDataParser {
+
+ protected int getVersion() {
+ return 1;
+ }
+
+ /**
+ * The maximum number of columns (data keys) passed to the parser or found in the file
+ * for a given loop_ or category.subkey listing.
+ *
+ */
+ public static final int KEY_MAX = 100;
+
+ private GenericLineReader reader;
+ private BufferedReader br;
+
+ /**
+ * from buffered reader
+ */
+ protected String line;
+
+ /**
+ * working string (buffer)
+ *
+ */
+ protected String str;
+
+ /**
+ * pointer to current character on str
+ */
+ protected int ich;
+
+ /**
+ * length of str
+ *
+ */
+ protected int cch;
+
+ /**
+ * whether we are processing an unquoted value or key
+ */
+ protected boolean wasUnquoted;
+
+ /**
+ * optional token terminator; in CIF 2.0 could be } or ]
+ */
+ protected char cterm = '\0';
+
+ /**
+ * string to return for CIF data value . and ?
+ */
+ protected String nullString = "\0";
+
+ /**
+ * A flag to create and return Java objects, not strings.
+ * Used only by Jmol scripting x = getProperty("cifInfo", filename).
+ */
+ protected boolean asObject;
+
+
+ /**
+ * debugging flag passed from reader; unused
+ *
+ */
+ protected boolean debugging;
+
+
+ /**
+ * private processing fields
+ *
+ */
+ private Object strPeeked;
+ private int ichPeeked;
+ private int columnCount;
+ private String[] columnNames;
+ private Object[] columnData = new Object[KEY_MAX];
+ private boolean isLoop;
+ private boolean haveData;
+
+ /**
+ * comments at the top of a file, including #\#CIF_2.0, for example
+ */
+ private SB fileHeader = new SB();
+ private boolean isHeader = true;
+
+
+ /**
+ * Set the string value of what is returned for "." and "?"
+ *
+ * @param nullString null here returns "." and "?"; default is "\0"
+ *
+ */
+ public void setNullValue(String nullString) {
+ this.nullString = nullString;
+ }
+
+ /**
+ * A global, static map that contains field information. The assumption is that
+ * if we read a set of fields for, say, atom_site, once in a lifetime, then
+ * that should be good forever. Those are static lists. Or should be....
+ */
+ private static Map<String, Integer> htFields = new Hashtable<String, Integer>();
+
+ ////////////////////////////////////////////////////////////////
+ // special tokenizer class
+ ////////////////////////////////////////////////////////////////
+
+ public CifDataParser() {
+ // for reflection
+ }
+
+ @Override
+ public Object getColumnData(int i) {
+ return columnData[i];
+ }
+
+ @Override
+ public int getColumnCount() {
+ return columnCount;
+ }
+
+ @Override
+ public String getColumnName(int i) {
+ return columnNames[i];
+ }
+
+ /**
+ * A Chemical Information File data parser.
+ *
+ * set() should be called immediately upon construction.
+ *
+ * Two options; one of reader or br should be null, or reader will be
+ * ignored. Just simpler this way...
+ *
+ * @param reader Anything that can deliver a line of text or null
+ * @param br A standard BufferedReader.
+ * @param debugging
+ *
+ */
+ @Override
+ public CifDataParser set(GenericLineReader reader, BufferedReader br, boolean debugging) {
+ this.reader = reader;
+ this.br = br;
+ this.debugging = debugging;
+ return this;
+ }
+
+
+ /**
+ *
+ * @return commented-out section at the start of a CIF file.
+ *
+ */
+ @Override
+ public String getFileHeader() {
+ return fileHeader.toString();
+ }
+
+
+ /**
+ * Parses all CIF data for a reader defined in the constructor
+ * into a standard Map structure and close the BufferedReader if
+ * it exists.
+ *
+ * @return Hashtable of models Vector of Hashtable data
+ */
+ @Override
+ public Map<String, Object> getAllCifData() {
+ line = "";
+ String key;
+ Map<String, Object> data = null, data0 = null;
+ Map<String, Object> allData = new Hashtable<String, Object>();
+ Lst<Map<String, Object>> models = new Lst<Map<String,Object>>();
+ allData.put("models", models);
+ asObject = (getVersion() >= 2);
+ nullString = null;
+ Lst<Map<String, Object>> saveFrames = new Lst<Map<String, Object>>();
+ try {
+ while ((key = getNextToken()) != null) {
+ if (key.startsWith("global_") || key.startsWith("data_")) {
+ models.addLast(data0 = data = new Hashtable<String, Object>());
+ data.put("name", key);
+ continue;
+ }
+ if (key.startsWith("loop_")) {
+ getAllCifLoopData(data);
+ continue;
+ }
+ if (key.startsWith("save_")) {
+ if (key.equals("save_")) {
+ int n = saveFrames.size();
+ if (n == 0) {
+ System.out.println("CIF ERROR ? save_ without corresponding save_xxxx");
+ data = data0;
+ } else {
+ data = saveFrames.removeItemAt(n - 1);
+ }
+ } else {
+ saveFrames.addLast(data);
+ Map<String, Object> d = data;
+ data = new Hashtable<String, Object>();
+ d.put(key, data);
+ }
+ continue;
+ }
+ if (key.charAt(0) != '_') {
+ System.out.println("CIF ERROR ? should be an underscore: " + key);
+ } else {
+ Object value = (asObject ? getNextTokenObject() : getNextToken());
+ if (value == null) {
+ System.out.println("CIF ERROR ? end of file; data missing: " + key);
+ } else {
+ data.put(fixKey(key), value);
+ }
+ }
+ }
+ } catch (Exception e) {
+ // ?
+ }
+ asObject = false;
+ try {
+ if (br != null)
+ br.close();
+ } catch (Exception e) {
+ // ?
+ }
+ nullString = "\0";
+ return allData;
+ }
+
+ /**
+ * create our own list of keywords and for each one create a list
+ * of data associated with that keyword. For example, a list of all
+ * x coordinates, then a list of all y coordinates, etc.
+ *
+ * @param data
+ * @throws Exception
+ */
+ @SuppressWarnings("unchecked")
+ private void getAllCifLoopData(Map<String, Object> data) throws Exception {
+ String key;
+ Lst<String> keyWords = new Lst<String>();
+ Object o;
+ while ((o = peekToken()) != null && o instanceof String && ((String) o).charAt(0) == '_') {
+ key = fixKey((String) getTokenPeeked());
+ keyWords.addLast(key);
+ data.put(key, new Lst<String>());
+ }
+ columnCount = keyWords.size();
+ if (columnCount == 0)
+ return;
+ isLoop = true;
+ while (getData())
+ for (int i = 0; i < columnCount; i++)
+ ((Lst<Object>)data.get(keyWords.get(i))).addLast(columnData[i]);
+ isLoop = false;
+ }
+
+ @Override
+ public String readLine() {
+ try {
+ line = (reader == null ? br.readLine() : reader.readNextLine());
+ if (line == null)
+ return null;
+ if (isHeader) {
+ if (line.startsWith("#"))
+ fileHeader.append(line).appendC('\n');
+ else
+ isHeader = false;
+ }
+ return line;
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ /**
+ * The work horse; a general reader for loop data. Fills colunnData with
+ * fieldCount fields.
+ *
+ * @return false if EOF
+ * @throws Exception
+ */
+ @Override
+ public boolean getData() throws Exception {
+ // line is already present, and we leave with the next line to parse
+ if (isLoop) {
+ for (int i = 0; i < columnCount; ++i)
+ if ((columnData[i] = getNextDataToken()) == null)
+ return false;
+ } else if (haveData) {
+ haveData = false;
+ } else {
+ return false;
+ }
+ return (columnCount > 0);
+ }
+
+ /**
+ *
+ * Skips all associated loop data. (Skips to next control word.)
+ *
+ * @throws Exception
+ */
+ @Override
+ public String skipLoop(boolean doReport) throws Exception {
+ String str;
+ SB ret = (doReport ? new SB() : null);
+ int n = 0;
+ while ((str = (String) peekToken()) != null && str.charAt(0) == '_') {
+ if (ret != null)
+ ret.append(str).append("\n");
+ getTokenPeeked();
+ n++;
+ }
+ if (n == 0)
+ n = columnCount; // end-of-label-section skip
+ int m = 0;
+ while ((str = (String) getNextDataToken()) != null) {
+ if (ret == null)
+ continue;
+ ret.append(str).append(" ");
+ if ((++m % n) == 0)
+ ret.append("\n");
+ }
+ return (ret == null ? null : ret.toString());
+ }
+
+ /**
+ * Get a token as a String value (for the reader)
+ *
+ * @return the next token of any kind, or null
+ * @throws Exception
+ */
+ @Override
+ public String getNextToken() throws Exception {
+ wasUnquoted = true;
+ return (String) getNextTokenProtected();
+ }
+
+ /**
+ * Get the token as a Java Object
+ *
+ * @return the next token of any kind, or null
+ * @throws Exception
+ */
+ public Object getNextTokenObject() throws Exception {
+ wasUnquoted = true;
+ return getNextTokenProtected();
+ }
+
+ /**
+ * Just makes sure
+ * @return String from buffer.
+ * @throws Exception
+ */
+ protected Object getNextTokenProtected() throws Exception {
+ return (getNextLine() ? nextStrToken() : null);
+ }
+
+ /**
+ *
+ * first checks to see if the next token is an unquoted
+ * control code, and if so, returns null
+ *
+ * @return next data token or null
+ * @throws Exception
+ */
+ @Override
+ public Object getNextDataToken() throws Exception {
+ Object o = peekToken();
+ if (o == null)
+ return null;
+ if (wasUnquoted && o instanceof String) {
+ String str = (String) o;
+ if (str.charAt(0) == '_' || str.startsWith("loop_")
+ || str.startsWith("data_")
+ || str.startsWith("save_")
+ || str.startsWith("stop_")
+ || str.startsWith("global_"))
+ return null;
+ }
+ return getTokenPeeked();
+ }
+
+ /**
+ * Just look at the next token. Saves it for retrieval
+ * using getTokenPeeked()
+ *
+ * @return next token or null if EOF
+ * @throws Exception
+ */
+ @Override
+ public Object peekToken() throws Exception {
+ if (!getNextLine())
+ return null;
+ int ich = this.ich;
+ strPeeked = nextStrToken();
+ ichPeeked= this.ich;
+ this.ich = ich;
+ return strPeeked;
+ }
+
+ /**
+ * grab a new line if necessary and prepare it
+ * if it starts with ";"
+ *
+ * @return updated this.str
+ * @throws Exception
+ */
+ private boolean getNextLine() throws Exception {
+ while (!strHasMoreTokens())
+ if (prepareNextLine() == null)
+ return false;
+ return true;
+ }
+
+ /**
+ *
+ * @return the token last acquired; may be null
+ */
+ @Override
+ public Object getTokenPeeked() {
+ ich = ichPeeked;
+ return strPeeked;
+ }
+
+ /**
+ * Used especially for data that might be multi-line data that
+ * might have unwanted white space at start or end.
+ *
+ * @param str
+ * @return str without any leading/trailing white space, and no '\n'
+ */
+ @Override
+ public String fullTrim(String str) {
+ int pt0 = -1;
+ int pt1 = str.length();
+ while (++pt0 < pt1 && PT.isWhitespace(str.charAt(pt0))) {
+ }
+ while (--pt1 > pt0 && PT.isWhitespace(str.charAt(pt1))) {
+ }
+ return str.substring(pt0, pt1 + 1);
+ }
+
+ private final static String grABC =
+ "ABX\u0394E\u03A6\u0393H" // ABCDEFGH
+ + "I_K\u039BMNO\u03A0" // I_KLMNOP
+ + "\u0398P\u03A3TY_\u03A9\u039E\u03A5Z"; // QRSTU_WXYZ
+ private final static String grabc =
+ "\u03B1\u03B2\u03C7\u03A4\u03A5\u03C6\u03B3\u03B7" // abcdefgh
+ + "\u03B9_\u03BA\u03BB\u03BC\u03BD\u03BF\u03C0" // i_klmnop
+ + "\u03B8\u03C1\u03C3\u03C4\u03C5_\u03C9\u03BE\u03C5\u03B6"; // qrstu_wxyz
+
+ /**
+ * Only translating the basic Greek set here, not all the other stuff. See
+ * http://www.iucr.org/resources/cif/spec/version1.1/semantics#markup
+ *
+ * @param data
+ * @return cleaned string
+ */
+ @Override
+ public String toUnicode(String data) {
+ int pt;
+ try {
+ while ((pt = data.indexOf('\\')) >= 0) {
+ int c = data.charAt(pt + 1);
+ String ch = (c >= 65 && c <= 90 ? grABC.substring(c - 65, c - 64)
+ : c >= 97 && c <= 122 ? grabc.substring(c - 97, c - 96) : "_");
+ data = data.substring(0, pt) + ch + data.substring(pt + 2);
+ }
+ } catch (Exception e) {
+ // ignore
+ }
+
+ return data;
+ }
+
+ /**
+ * Process a data block, with or without a loop_.
+ *
+ * Passed an array of field names, this method fills two int[] arrays. The
+ * first, key2col, maps desired key values to actual order of appearance
+ * (column number) in the file; the second, col2key, is a reverse loop-up for
+ * that, mapping column numbers to desired field indices.
+ *
+ * When called within a loop_ context, this.columnData will be created but not filled.
+ *
+ * Alternatively, if fields is null, then this.fieldNames is
+ * filled, in order, with key data, and both key2col and col2key will be
+ * simply 0,1,2,... This array is used in cases such as matrices for which
+ * there are simply too many possibilities to list, and the key name itself
+ * contains information that we need.
+ *
+ * When not a loop_ context, keys are expected to be in the mmCIF form
+ * category.subkey and will be unique within a data block (see
+ * http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html).
+ * Keys and data will be read for all data in the same category, filling this.columnData.
+ *
+ *
+ * In this way, the calling class does not need to enumerate all possible
+ * category names, but instead can focus on just those of interest.
+ *
+ *
+ * @param fields
+ * list of normalized field names, such as
+ * "_pdbx_struct_assembly_gen_assembly_id" (with "_" instead of ".")
+ * @param key
+ * null to indicate a loop_ construct, otherwise the initial category.subkey
+ * found
+ * @param data
+ * when not loop_ the initial data read, otherwise ignored
+ * @param key2col
+ * map of desired keys to actual columns
+ * @param col2key
+ * map of actual columns to desired keys
+ * @throws Exception
+ */
+ @Override
+ public void parseDataBlockParameters(String[] fields, String key,
+ String data, int[] key2col, int[] col2key) throws Exception {
+ isLoop = (key == null);
+ Object o;
+ String s;
+ if (fields == null) {
+ // for reading full list of keys, as for matrices
+ columnNames = new String[KEY_MAX];
+ } else {
+ if (!htFields.containsKey(fields[0]))
+ for (int i = fields.length; --i >= 0;)
+ htFields.put(fields[i], Integer.valueOf(i));
+ for (int i = fields.length; --i >= 0;)
+ key2col[i] = NONE;
+ }
+ columnCount = 0;
+ int pt, i;
+ if (isLoop) {
+ while (true) {
+ o = peekToken();
+ if (o == null) {
+ // we are PREMATURELY done; reset
+ columnCount = 0;
+ break;
+ }
+ // end of the loop is a new token not starting with underscore
+ if (!(o instanceof String) || ((String) o).charAt(0) != '_')
+ break;
+
+ pt = columnCount++;
+ s = fixKey((String) getTokenPeeked());
+ if (fields == null) {
+ // just make a linear model, saving the list
+ columnNames[col2key[pt] = key2col[pt] = pt] = s;
+ continue;
+ }
+ Integer iField = htFields.get(s);
+ i = (iField == null ? NONE : iField.intValue());
+ if ((col2key[pt] = i) != NONE)
+ key2col[i] = pt;
+ }
+ } else {
+ pt = key.indexOf(".");
+ String str0 = (pt < 0 ? key : key.substring(0, pt + 1));
+ while (true) {
+ // end of the loop is a new token not starting with underscore
+ pt = columnCount++;
+ if (key == null) {
+ key = (String) getTokenPeeked();
+ data = getNextToken();
+ }
+ Integer iField = htFields.get(fixKey(key));
+ i = (iField == null ? NONE : iField.intValue());
+ if ((col2key[pt] = i) != NONE)
+ columnData[key2col[i] = pt] = data;
+ if ((o = peekToken()) == null || !(o instanceof String) || !((String) o).startsWith(str0))
+ break;
+ key = null;
+ }
+ haveData = (columnCount > 0);
+ }
+ }
+
+ @Override
+ public String fixKey(String key) {
+ // PRELIMINARY -- BilBao _magnetic
+ // PRELIMINARY -- Jana2006
+ return (PT.rep(
+ key.startsWith("_magnetic") ? key.substring(9)
+ : key.startsWith("_jana") ? key.substring(5)
+ : key, ".", "_").toLowerCase());
+ }
+
+ //////////////////// private methods ////////////////////
+
+
+ /**
+ * sets global str and line to be parsed from the beginning
+ *
+ * \1 .... \1 indicates an embedded fully escaped data object
+ *
+ * @param str new data string
+ * @return str
+ */
+ protected String setString(String str) {
+ this.str = line = str;
+ cch = (str == null ? 0 : str.length());
+ ich = 0;
+ return str;
+ }
+
+ /*
+ * http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax
+ *
+ * 17. The special sequence of end-of-line followed
+ * immediately by a semicolon in column one (denoted "<eol>;")
+ * may also be used as a delimiter at the beginning and end
+ * of a character string comprising a data value. The complete
+ * bounded string is called a text field, and may be used to
+ * convey multi-line values. The end-of-line associated with
+ * the closing semicolon does not form part of the data value.
+ * Within a multi-line text field, leading white space within
+ * text lines must be retained as part of the data value; trailing
+ * white space on a line may however be elided.
+ *
+ * 18. A text field delimited by the <eol>; digraph may not
+ * include a semicolon at the start of a line of text as
+ * part of its value.
+ *
+ * 20. For example, the data value foo may be expressed
+ * equivalently as an unquoted string foo, as a quoted
+ * string 'foo' or as a text field
+ *
+ *;foo
+ *;
+ *
+ * By contrast the value of the text field
+ *
+ *; foo
+ * bar
+ *;
+ *
+ * is foo<eol> bar (where <eol> represents an end-of-line);
+ * the embedded space characters are significant.
+ *
+ *
+ * I (BH) note, however, that we sometimes have:
+ *
+ * _some_name
+ * ;
+ * the name here
+ * ;
+ *
+ * so this should actually be
+ *
+ * ;the name here
+ * ;
+ *
+ * for this, we use fullTrim();
+ *
+ */
+
+ /**
+ *
+ * sets the string for parsing to be from the next line
+ * when the token buffer is empty, and if ';' is at the
+ * beginning of that line, extends the string to include
+ * that full multiline string. Uses \1 to indicate that
+ * this is a special quotation.
+ *
+ *
+ *
+ * @return the next line or null if EOF
+ * @throws Exception
+ */
+ protected String prepareNextLine() throws Exception {
+ setString(readLine());
+ if (line == null || line.length() == 0)
+ return line;
+ if (line.charAt(0) == ';')
+ return preprocessString();
+ if (str.startsWith("###non-st#"))
+ ich = 10;
+ return line;
+ }
+
+ /**
+ * Preprocess the string on a line starting with a semicolon
+ * to produce a string with a \1 ... \1 segment
+ * that will be picked up in the next round
+ *
+ * @return escaped part with attached extra data
+ * @throws Exception
+ */
+ protected String preprocessString() throws Exception {
+ return setString(preprocessSemiString());
+ }
+
+ /**
+ * Encapsulate a multi-line ; .... ; string with \1 ... \1
+ *
+ * CIF 1.0 and CIF 2.0
+ *
+ * @return ecapsulated string
+ * @throws Exception
+ */
+ protected String preprocessSemiString() throws Exception {
+ ich = 1;
+ String str = '\1' + line.substring(1) + '\n';
+ while (readLine() != null) {
+ if (line.startsWith(";")) {
+ // remove trailing <eol> only, and attach rest of next line
+ str = str.substring(0, str.length() - 1)
+ + '\1' + line.substring(1);
+ break;
+ }
+ str += line + '\n';
+ }
+ return str;
+ }
+
+ /**
+ * @return TRUE if there are more tokens in the line buffer
+ *
+ */
+ private boolean strHasMoreTokens() {
+ if (str == null)
+ return false;
+ char ch = '#';
+ while (ich < cch && ((ch = str.charAt(ich)) == ' ' || ch == '\t'))
+ ++ich;
+ return (ich < cch && ch != '#');
+ }
+
+ /**
+ * assume that hasMoreTokens() has been called and that ich is pointing at a
+ * non-white character. Also sets boolean wasUnQuoted, because we need to know
+ * if we should be checking for a control keyword. 'loop_' is different from
+ * just loop_ without the quotes.
+ *
+ * @return null if no more tokens, "\0" if '.' or '?', or next token
+ */
+ private Object nextStrToken() {
+ if (ich == cch)
+ return null;
+ char ch = str.charAt(ich);
+ if (isQuote(ch)) {
+ wasUnquoted = false;
+ return getQuotedStringOrObject(ch);
+ }
+ int ichStart = ich;
+ wasUnquoted = true;
+ while (ich < cch && !isTerminator(ch = str.charAt(ich)))
+ ++ich;
+ if (ich == ichStart + 1)
+ if (nullString != null
+ && (str.charAt(ichStart) == '.' || str.charAt(ichStart) == '?'))
+ return nullString;
+ String s = str.substring(ichStart, ich);
+ return unquoted(s);
+ }
+
+ /**
+ * In CIF 2.0, this method turns a String into an Integer or Float
+ * In CIF 1.0 (here) just return the unchanged value.
+ * @param s unquoted string
+ * @return unchanged value
+ */
+ protected Object unquoted(String s) {
+ return s;
+ }
+
+ /**
+ * The token terminator is space or tab in CIF 1.0,
+ * but it can be quoted strings in CIF 2.0.
+ *
+ * @param c
+ * @return true if this character is a terminator
+ */
+ protected boolean isTerminator(char c) {
+ return c == ' ' || c == '\t' || c == cterm ;
+ }
+
+ /**
+ * CIF 1.0 only; we handle various quote types here
+ * @param ch
+ * @return true if this character is a (starting) quote
+ */
+ protected boolean isQuote(char ch) {
+ switch (ch) {
+ case '\'':
+ case '\"':
+ case '\1':
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * CIF 1.0 only.
+ *
+ *
+ * @param ch current character being pointed to
+ * @return a String data object
+ */
+ protected Object getQuotedStringOrObject(char ch) {
+ int ichStart = ich;
+ char chClosingQuote = ch;
+ boolean wasQuote = false;
+ while (++ich < cch) {
+ ch = str.charAt(ich);
+ // CIF 1.0 rules require that the closing ' or "" be followed by space or tab or EOL
+ if (wasQuote && (ch == ' ' || ch == '\t'))
+ break;
+ wasQuote = (ch == chClosingQuote);
+ }
+ int pt1 = ichStart + 1;
+ int pt2 = ich - 1;
+ if (ich == cch && !wasQuote) {
+ // reached the end of the string without finding closing '
+ // so take the whole thing. Probably a bad CIF file.
+ pt1--;
+ pt2++;
+ } else {
+ // throw away the last white character
+ ++ich;
+ }
+ return str.substring(pt1, pt2);
+ }
+
+
+}
\ No newline at end of file
--- /dev/null
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2011 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package javajs.util;
+
+
+class CompoundDocDirEntry {
+
+ private final CompoundDocument cd;
+
+ /**
+ * @param compoundDocument
+ */
+ CompoundDocDirEntry(CompoundDocument compoundDocument) {
+ cd = compoundDocument;
+ }
+
+ // 128 bytes
+ //offset 0:
+ byte[] unicodeName64 = new byte[64];
+ short nBytesUnicodeName; // twice the ascii length, including terminating 0
+ byte entryType; // 0 empty; 1 storage; 2 stream; 5 root storage
+ //byte entryColor; // 0 red or 1 black
+ //int DIDchildLeft;
+ //int DIDchildRight;
+ //int DIDstorageRoot;
+ byte[] uniqueID16 = new byte[16];
+ byte[] userflags4 = new byte[4];
+ //long timeStamp1;
+ //long timeStamp2;
+ //offset 116:
+ int SIDfirstSector; // either SAT or SSAT
+ int lenStream;
+ byte[] unused = new byte[8];
+
+ // derived:
+
+ String entryName;
+ boolean isStandard;
+ boolean isEmpty;
+
+ final boolean readData() {
+ try {
+ cd.readByteArray(unicodeName64, 0, 64);
+ nBytesUnicodeName = cd.readShort();
+ entryType = cd.readByte();
+ /*entryColor = */cd.readByte();
+ /*DIDchildLeft = */cd.readInt();
+ /*DIDchildRight = */cd.readInt();
+ /*DIDstorageRoot = */cd.readInt();
+ cd.readByteArray(uniqueID16, 0, 16);
+ cd.readByteArray(userflags4, 0, 4);
+ /*timeStamp1 = */ cd.readByteArray(unused, 0, 8);//cd.readLong();
+ /*timeStamp2 = */ cd.readByteArray(unused, 0, 8);//cd.readLong();
+ //offset 116:
+ SIDfirstSector = cd.readInt();
+ lenStream = cd.readInt();
+ cd.readByteArray(unused, 0, 4);
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ return false;
+ }
+ entryName = "";
+ for (int i = 0; i < nBytesUnicodeName - 2; i += 2)
+ entryName += (char) unicodeName64[i];
+ isStandard = (entryType == 5 || lenStream >= cd.header.minBytesStandardStream);
+ isEmpty = (entryType == 0 || lenStream <= 0);
+ //System.out.println(entryName + " type " + entryType);
+ return true;
+ }
+}
\ No newline at end of file
--- /dev/null
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2011 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package javajs.util;
+
+
+class CompoundDocHeader {
+
+ /**
+ *
+ */
+ private final CompoundDocument cd;
+
+ /**
+ * @param compoundDocument
+ */
+ CompoundDocHeader(CompoundDocument compoundDocument) {
+ cd = compoundDocument;
+ }
+
+ //512 bytes
+ //offset 0:
+ byte[] magicNumbers = new byte[8]; // D0CF11E0A1B11AE1
+ byte[] uniqueID16 = new byte[16];
+ byte revNumber; // 3E = 62
+ //byte unusedb1;
+ byte verNumber; // 3
+ //byte unusedb2;
+ //short byteOrder; // -2 littleEndian
+ short sectorPower; // 2^sectorPower = sector size; 512 = 2^9
+ short shortSectorPower; // 2^shortSectorPower = short sector size; 64 = 2^6
+ byte[] unused = new byte[10];
+ int nSATsectors; // number of sectors for sector allocation table
+ int SID_DIR_start; // sector identifier of start of directory sector
+ //offset 56:
+ int minBytesStandardStream; // less than this (and not DIR) will be "short"
+ int SID_SSAT_start; // start of short sector allocation table (SSAT)
+ int nSSATsectors; // number of sectors allocated to SSAT
+ int SID_MSAT_next; // pointer to next master sector allocation table sector
+ int nAdditionalMATsectors; // number of sectors allocated to more MSAT sectors
+ //offset 76; 436 bytes:
+ int[] MSAT0 = new int[109]; // beginning of master allocation table
+
+ /*
+ * Sector 0 is first sector AFTER this header
+ *
+ * If sectorPower = 9, then this allows for 109 PAGES
+ * of sector allocation tables, with 127 pointers per
+ * page (plus 1 pointer to the next SAT page), each
+ * pointing to a sector of 512 bytes. Thus, with no additional
+ * MSAT pages, the header allows for 109*128*512 = 7.1 Mb file
+ *
+ */
+
+ final boolean readData() {
+ try {
+ cd.readByteArray(magicNumbers, 0, 8);
+ if ((magicNumbers[0] & 0xFF) != 0xD0 || (magicNumbers[1] & 0xFF) != 0xCF
+ || (magicNumbers[2] & 0xFF) != 0x11 || (magicNumbers[3] & 0xFF) != 0xE0
+ || (magicNumbers[4] & 0xFF) != 0xA1 || (magicNumbers[5] & 0xFF) != 0xB1
+ || (magicNumbers[6] & 0xFF) != 0x1A || (magicNumbers[7] & 0xFF) != 0xE1)
+ return false;
+ cd.readByteArray(uniqueID16, 0, 16);
+ revNumber = cd.readByte();
+ cd.readByte();
+ verNumber = cd.readByte();
+ cd.readByte();
+ byte b1 = cd.readByte();
+ byte b2 = cd.readByte();
+ cd.isBigEndian = (b1 == -1 && b2 == -2);
+ sectorPower = cd.readShort();
+ shortSectorPower = cd.readShort();
+ cd.readByteArray(unused, 0, 10);
+ nSATsectors = cd.readInt();
+ SID_DIR_start = cd.readInt();
+ cd.readByteArray(unused, 0, 4);
+ minBytesStandardStream = cd.readInt();
+ SID_SSAT_start = cd.readInt();
+ nSSATsectors = cd.readInt();
+ SID_MSAT_next = cd.readInt();
+ nAdditionalMATsectors = cd.readInt();
+ for (int i = 0; i < 109; i++)
+ MSAT0[i] = cd.readInt();
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ return false;
+ }
+ return true;
+ }
+}
\ No newline at end of file
--- /dev/null
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2006-03-18 15:59:33 -0600 (Sat, 18 Mar 2006) $
+ * $Revision: 4652 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: hansonr@stolaf.edu
+ *
+ * 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 Public 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 javajs.util;
+
+
+import java.io.DataInputStream;
+import java.io.BufferedInputStream;
+
+
+import java.util.Map;
+
+import javajs.api.GenericZipTools;
+
+
+
+/* a simple compound document reader.
+ *
+ * DIRECTORY STRUCTURE IS NOT REGENERATED
+ *
+ * See http://sc.openoffice.org/compdocfileformat.pdf
+ *
+ * random access file info:
+ * http://java.sun.com/docs/books/tutorial/essential/io/rafs.html
+ *
+ * SHOOT! random access is only for applications, not applets!
+ *
+ * With a bit more work, this could be set up to deliver binary files, but
+ * right now I've only implemented it for string-based data.
+ *
+ */
+
+public class CompoundDocument extends BinaryDocument{
+
+// RandomAccessFile file;
+ CompoundDocHeader header = new CompoundDocHeader(this);
+ Lst<CompoundDocDirEntry> directory = new Lst<CompoundDocDirEntry>();
+ CompoundDocDirEntry rootEntry;
+
+ protected GenericZipTools jzt;
+
+ int[] SAT;
+ int[] SSAT;
+ int sectorSize;
+ int shortSectorSize;
+ int nShortSectorsPerStandardSector;
+ int nIntPerSector;
+ int nDirEntriesperSector;
+
+ // called by reflection
+
+ public CompoundDocument(){
+ super();
+ this.isBigEndian = true;
+ }
+
+ public void setDocStream(GenericZipTools jzt, BufferedInputStream bis) {
+ this.jzt = jzt;
+ if (!isRandom) {
+ stream = new DataInputStream(bis);
+ }
+ stream.mark(Integer.MAX_VALUE);
+ if (!readHeader())
+ return;
+ getSectorAllocationTable();
+ getShortSectorAllocationTable();
+ getDirectoryTable();
+ }
+
+ public Lst<CompoundDocDirEntry> getDirectory() {
+ return directory;
+ }
+
+ public String getDirectoryListing(String separator) {
+ SB sb = new SB();
+ for (int i = 0; i < directory.size(); i++) {
+ CompoundDocDirEntry thisEntry = directory.get(i);
+ if (!thisEntry.isEmpty)
+ sb.append(separator).append(thisEntry.entryName)
+ .append("\tlen=").appendI(thisEntry.lenStream)
+ .append("\tSID=").appendI(thisEntry.SIDfirstSector)
+ .append(thisEntry.isStandard ? "\tfileOffset="
+ + getOffset(thisEntry.SIDfirstSector) : "");
+ }
+ return sb.toString();
+ }
+
+ public SB getAllData() {
+ return getAllDataFiles(null, null);
+ }
+
+ /**
+ * reads a compound document directory and saves all data in a Hashtable
+ * so that the files may be organized later in a different order. Also adds
+ * a #Directory_Listing entry.
+ *
+ * Files are bracketed by BEGIN Directory Entry and END Directory Entry lines,
+ * similar to ZipUtil.getAllData.
+ *
+ * @param prefix
+ * @param binaryFileList |-separated list of files that should be saved
+ * as xx xx xx hex byte strings. The directory listing
+ * is appended with ":asBinaryString"
+ * @param fileData
+ */
+ @Override
+ public void getAllDataMapped(String prefix,
+ String binaryFileList, Map<String, String> fileData) {
+ fileData.put("#Directory_Listing", getDirectoryListing("|"));
+ binaryFileList = "|" + binaryFileList + "|";
+ for (int i = 0; i < directory.size(); i++) {
+ CompoundDocDirEntry thisEntry = directory.get(i);
+ if (!thisEntry.isEmpty && thisEntry.entryType != 5) {
+ String name = thisEntry.entryName;
+ System.out.println("CompoundDocument file " + name);
+ boolean isBinary = (binaryFileList.indexOf("|" + name + "|") >= 0);
+ if (isBinary)
+ name += ":asBinaryString";
+ fileData.put(prefix + "/" + name, appendData(new SB(), name, thisEntry, isBinary).toString());
+ }
+ }
+ close();
+ }
+
+ @Override
+ public SB getAllDataFiles(String binaryFileList, String firstFile) {
+// firstFile is now ignored
+// if (firstFile != null) {
+// for (int i = 0; i < directory.size(); i++) {
+// CompoundDocDirEntry thisEntry = directory.get(i);
+// if (thisEntry.entryName.equals(firstFile)) {
+// directory.remove(i);
+// directory.add(1, thisEntry); // after ROOT_ENTRY
+// break;
+// }
+// }
+// }
+ SB data = new SB();
+ data.append("Compound Document File Directory: ");
+ data.append(getDirectoryListing("|"));
+ data.append("\n");
+ CompoundDocDirEntry thisEntry;
+ binaryFileList = "|" + binaryFileList + "|";
+ for (int i = 0, n = directory.size(); i < n; i++) {
+ thisEntry = directory.get(i);
+ //System.out.println("CompoundDocument reading " + thisEntry.entryName);
+ String name = thisEntry.entryName;
+ switch (thisEntry.entryType) {
+ case 5: // root
+ break;
+ case 1: // user storage (dir)
+ data.append("NEW Directory ").append(name).append("\n");
+ break;
+ case 2: // user stream (file)
+ if (name.endsWith(".gz"))
+ name = name.substring(0, name.length() - 3);
+ appendData(data, name, thisEntry, binaryFileList.indexOf("|" + thisEntry.entryName + "|") >= 0);
+ break;
+ }
+ }
+ close();
+ return data;
+ }
+
+ private SB appendData(SB data, String name, CompoundDocDirEntry thisEntry,
+ boolean isBinary) {
+ data.append("BEGIN Directory Entry ").append(name).append("\n");
+ data.appendSB(getEntryAsString(thisEntry, isBinary));
+ data.append("\nEND Directory Entry ").append(name).append("\n");
+ return data;
+ }
+
+ public SB getFileAsString(String entryName) {
+ for (int i = 0; i < directory.size(); i++) {
+ CompoundDocDirEntry thisEntry = directory.get(i);
+ if (thisEntry.entryName.equals(entryName))
+ return getEntryAsString(thisEntry, false);
+ }
+ return new SB();
+ }
+
+ private long getOffset(int SID) {
+ return (SID + 1) * sectorSize;
+ }
+
+ private void gotoSector(int SID) {
+ seek(getOffset(SID));
+ }
+
+ private boolean readHeader() {
+ if (!header.readData())
+ return false;
+ sectorSize = 1 << header.sectorPower;
+ shortSectorSize = 1 << header.shortSectorPower;
+ nShortSectorsPerStandardSector = sectorSize / shortSectorSize; // e.g. 512 / 64 = 8
+ nIntPerSector = sectorSize / 4; // e.g. 512 / 4 = 128
+ nDirEntriesperSector = sectorSize / 128; // e.g. 512 / 128 = 4
+// System.out.println(
+// "compound document: revNum=" + header.revNumber +
+// " verNum=" + header.verNumber + " isBigEndian=" + isBigEndian +
+// " bytes per standard/short sector=" + sectorSize + "/" + shortSectorSize);
+ return true;
+ }
+
+ private void getSectorAllocationTable() {
+ int nSID = 0;
+ int thisSID;
+ SAT = new int[header.nSATsectors * nIntPerSector + 109];
+
+ try {
+ for (int i = 0; i < 109; i++) {
+ thisSID = header.MSAT0[i];
+ if (thisSID < 0)
+ break;
+ gotoSector(thisSID);
+ for (int j = 0; j < nIntPerSector; j++) {
+ SAT[nSID++] = readInt();
+ //Logger.debug(thisSID+"."+j + "/" + (nSID - 1) + " : " + SAT[nSID - 1]);
+ }
+ }
+ int nMaster = header.nAdditionalMATsectors;
+ thisSID = header.SID_MSAT_next;
+ int[] MSAT = new int[nIntPerSector];
+ out: while (nMaster-- > 0 && thisSID >= 0) {
+ // read a page of sector identifiers pointing to SAT sectors
+ gotoSector(thisSID);
+ for (int i = 0; i < nIntPerSector; i++)
+ MSAT[i] = readInt();
+ // read each page of SAT sector identifiers
+ // last entry is pointer to next master sector allocation table page
+ for (int i = 0; i < nIntPerSector - 1; i++) {
+ thisSID = MSAT[i];
+ if (thisSID < 0)
+ break out;
+ gotoSector(thisSID);
+ for (int j = nIntPerSector; --j >= 0;)
+ SAT[nSID++] = readInt();
+ }
+ thisSID = MSAT[nIntPerSector - 1];
+ }
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ }
+ }
+
+ private void getShortSectorAllocationTable() {
+ int nSSID = 0;
+ int thisSID = header.SID_SSAT_start;
+ int nMax = header.nSSATsectors * nIntPerSector;
+ SSAT = new int[nMax];
+ try {
+ while (thisSID > 0 && nSSID < nMax) {
+ gotoSector(thisSID);
+ for (int j = 0; j < nIntPerSector; j++) {
+ SSAT[nSSID++] = readInt();
+ //System.out.println("short: " + thisSID+"."+j+" SSID=" +(nSSID-1)+" "+SSAT[nSSID-1]);
+ }
+ thisSID = SAT[thisSID];
+ }
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ }
+ }
+
+ private void getDirectoryTable() {
+ int thisSID = header.SID_DIR_start;
+ CompoundDocDirEntry thisEntry;
+ rootEntry = null;
+ try {
+ while (thisSID > 0) {
+ gotoSector(thisSID);
+ for (int j = nDirEntriesperSector; --j >= 0;) {
+ thisEntry = new CompoundDocDirEntry(this);
+ thisEntry.readData();
+ directory.addLast(thisEntry);
+ if (thisEntry.entryType == 5)
+ rootEntry = thisEntry;
+ }
+ thisSID = SAT[thisSID];
+ }
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ }
+// System.out.println("CompoundDocument directory entry: \n"
+// + getDirectoryListing("\n"));
+ }
+
+ private SB getEntryAsString(CompoundDocDirEntry thisEntry, boolean asBinaryString) {
+ if(thisEntry.isEmpty)
+ return new SB();
+ //System.out.println(thisEntry.entryName + " " + thisEntry.entryType + " " + thisEntry.lenStream + " " + thisEntry.isStandard + " " + thisEntry.SIDfirstSector);
+ return (thisEntry.isStandard ? getStandardStringData(
+ thisEntry.SIDfirstSector, thisEntry.lenStream, asBinaryString)
+ : getShortStringData(thisEntry.SIDfirstSector, thisEntry.lenStream, asBinaryString));
+ }
+ private SB getStandardStringData(int thisSID, int nBytes,
+ boolean asBinaryString) {
+ SB data = new SB();
+ byte[] byteBuf = new byte[sectorSize];
+ ZipData gzipData = new ZipData(nBytes);
+ try {
+ while (thisSID > 0 && nBytes > 0) {
+ gotoSector(thisSID);
+ nBytes = getSectorData(data, byteBuf, sectorSize, nBytes, asBinaryString, gzipData);
+ thisSID = SAT[thisSID];
+ }
+ if (nBytes == -9999)
+ return new SB();
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ }
+ if (gzipData.isEnabled)
+ gzipData.addTo(jzt, data);
+ return data;
+ }
+
+ private int getSectorData(SB data, byte[] byteBuf,
+ int nSectorBytes, int nBytes,
+ boolean asBinaryString, ZipData gzipData)
+ throws Exception {
+ readByteArray(byteBuf, 0, byteBuf.length);
+ int n = gzipData.addBytes(byteBuf, nSectorBytes, nBytes);
+ if (n >= 0)
+ return n;
+ if (asBinaryString) {
+ for (int i = 0; i < nSectorBytes; i++) {
+ data.append(Integer.toHexString(byteBuf[i] & 0xFF)).appendC(' ');
+ if (--nBytes < 1)
+ break;
+ }
+ } else {
+ for (int i = 0; i < nSectorBytes; i++) {
+ if (byteBuf[i] == 0)
+ return -9999; // don't allow binary data
+ data.appendC((char) byteBuf[i]);
+ if (--nBytes < 1)
+ break;
+ }
+ }
+ return nBytes;
+ }
+
+ private SB getShortStringData(int shortSID, int nBytes, boolean asBinaryString) {
+ SB data = new SB();
+ if (rootEntry == null)
+ return data;
+ int thisSID = rootEntry.SIDfirstSector;
+ int ptShort = 0;
+ byte[] byteBuf = new byte[shortSectorSize];
+ ZipData gzipData = new ZipData(nBytes);
+ try {
+ //System.out.println("CD shortSID=" + shortSID);
+ // point to correct short data sector, 512/64 = 4 per page
+ while (thisSID >= 0 && shortSID >= 0 && nBytes > 0) {
+ while (shortSID - ptShort >= nShortSectorsPerStandardSector) {
+ ptShort += nShortSectorsPerStandardSector;
+ thisSID = SAT[thisSID];
+ }
+ seek(getOffset(thisSID) + (shortSID - ptShort) * shortSectorSize);
+ nBytes = getSectorData(data, byteBuf, shortSectorSize, nBytes, asBinaryString, gzipData);
+ shortSID = SSAT[shortSID];
+ //System.out.println("CD shortSID=" + shortSID);
+ }
+ } catch (Exception e) {
+ System.out.println(data.toString());
+ System.out.println("reader error in CompoundDocument " + e.toString());
+ }
+ if (gzipData.isEnabled)
+ gzipData.addTo(jzt, data);
+ return data;
+ }
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-04-26 16:57:51 -0500 (Thu, 26 Apr 2007) $
+ * $Revision: 7502 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.util;
+
+/**
+ * created to remove ambiguities and make a simpler DecimalFormat
+ */
+public class DF {
+
+ private final static String[] formattingStrings = { "0", "0.0", "0.00",
+ "0.000", "0.0000", "0.00000", "0.000000", "0.0000000", "0.00000000",
+ "0.000000000" };
+ private final static String zeros = "0000000000000000000000000000000000000000";
+
+ private final static float[] formatAdds = { 0.5f, 0.05f, 0.005f, 0.0005f,
+ 0.00005f, 0.000005f, 0.0000005f, 0.00000005f, 0.000000005f, 0.0000000005f };
+
+ private final static Boolean[] useNumberLocalization = new Boolean[] { Boolean.TRUE };
+
+ public static void setUseNumberLocalization(boolean TF) {
+ useNumberLocalization[0] = (TF ? Boolean.TRUE : Boolean.FALSE);
+ }
+
+ public static String formatDecimalDbl(double value, int decimalDigits) {
+ if (decimalDigits == Integer.MAX_VALUE
+ || value == Double.NEGATIVE_INFINITY
+ || value == Double.POSITIVE_INFINITY
+ || Double.isNaN(value))
+ return "" + value;
+ return DF.formatDecimal((float) value, decimalDigits);
+ }
+
+ /**
+ * a simple alternative to DecimalFormat (which Java2Script does not have
+ * and which is quite too complex for our use here.)
+ *
+ * @param value
+ * @param decimalDigits
+ * @return formatted decimal
+ */
+ public static String formatDecimal(float value, int decimalDigits) {
+ if (decimalDigits == Integer.MAX_VALUE
+ || value == Float.NEGATIVE_INFINITY || value == Float.POSITIVE_INFINITY || Float.isNaN(value))
+ return "" + value;
+ int n;
+ if (decimalDigits < 0) {
+ decimalDigits = -decimalDigits;
+ if (decimalDigits > formattingStrings.length)
+ decimalDigits = formattingStrings.length;
+ if (value == 0)
+ return formattingStrings[decimalDigits] + "E+0";
+ //scientific notation
+ n = 0;
+ double d;
+ if (Math.abs(value) < 1) {
+ n = 10;
+ d = value * 1e-10;
+ } else {
+ n = -10;
+ d = value * 1e10;
+ }
+ String s = ("" + d).toUpperCase();
+ int i = s.indexOf("E");
+ n = PT.parseInt(s.substring(i + 1)) + n;
+ return (i < 0 ? "" + value : formatDecimal(PT.parseFloat(s.substring(
+ 0, i)), decimalDigits - 1)
+ + "E" + (n >= 0 ? "+" : "") + n);
+ }
+
+ if (decimalDigits >= formattingStrings.length)
+ decimalDigits = formattingStrings.length - 1;
+ String s1 = ("" + value).toUpperCase();
+ int pt = s1.indexOf(".");
+ if (pt < 0) // specifically JavaScript "-2" not "-2.0"
+ return s1 + formattingStrings[decimalDigits].substring(1);
+ boolean isNeg = s1.startsWith("-");
+ if (isNeg) {
+ s1 = s1.substring(1);
+ pt--;
+ }
+ int pt1 = s1.indexOf("E-");
+ if (pt1 > 0) {
+ n = PT.parseInt(s1.substring(pt1 + 1));
+ // 3.567E-2
+ // 0.03567
+ s1 = "0." + zeros.substring(0, -n - 1) + s1.substring(0, 1) + s1.substring(2, pt1);
+ pt = 1;
+ }
+
+ pt1 = s1.indexOf("E");
+ // 3.5678E+3
+ // 3567.800000000
+ // 1.234E10 %3.8f -> 12340000000.00000000
+ if (pt1 > 0) {
+ n = PT.parseInt(s1.substring(pt1 + 1));
+ s1 = s1.substring(0, 1) + s1.substring(2, pt1) + zeros;
+ s1 = s1.substring(0, n + 1) + "." + s1.substring(n + 1);
+ pt = s1.indexOf(".");
+ }
+ // "234.345667 len == 10; pt = 3
+ // " 0.0 " decimalDigits = 1
+
+ int len = s1.length();
+ int pt2 = decimalDigits + pt + 1;
+ if (pt2 < len && s1.charAt(pt2) >= '5') {
+ return formatDecimal(
+ value + (isNeg ? -1 : 1) * formatAdds[decimalDigits], decimalDigits);
+ }
+
+ SB sb = SB.newS(s1.substring(0, (decimalDigits == 0 ? pt
+ : ++pt)));
+ for (int i = 0; i < decimalDigits; i++, pt++) {
+ if (pt < len)
+ sb.appendC(s1.charAt(pt));
+ else
+ sb.appendC('0');
+ }
+ s1 = (isNeg ? "-" : "") + sb;
+ return (Boolean.TRUE.equals(useNumberLocalization[0]) ? s1 : s1.replace(',',
+ '.'));
+ }
+
+ /**
+ * an alternative to DecimalFormat "0.#"
+ *
+ * @param x
+ * @param precision
+ * @return formatted number
+ */
+ public static String formatDecimalTrimmed(double x, int precision) {
+ String str = formatDecimalDbl(x, precision);
+ int m = str.length() - 1;
+ char zero = '0';
+ while (m >= 0 && str.charAt(m) == zero)
+ m--;
+ return str.substring(0, m + 1); // 0.##...
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.StringReader;
+
+/**
+ * Just a simple abstract class to join a String reader and a String[]
+ * reader under the same BufferedReader umbrella.
+ *
+ * Subclassed as StringDataReader, ArrayDataReader, and ListDataReader
+ *
+ */
+
+public abstract class DataReader extends BufferedReader {
+
+ public abstract DataReader setData(Object data);
+
+ protected int ptMark;
+
+ public DataReader() {
+ super(new StringReader(""));
+ }
+
+ protected DataReader(Reader in) {
+ super(in);
+ }
+
+ public BufferedReader getBufferedReader() {
+ return this;
+ }
+
+ protected int readBuf(char[] buf, int off, int len) throws IOException {
+ // not used by StringDataReader
+ int nRead = 0;
+ String line = readLine();
+ if (line == null)
+ return 0;
+ int linept = 0;
+ int linelen = line.length();
+ for (int i = off; i < len && linelen >= 0; i++) {
+ if (linept >= linelen) {
+ linept = 0;
+ buf[i] = '\n';
+ line = readLine();
+ linelen = (line == null ? -1 : line.length());
+ } else {
+ buf[i] = line.charAt(linept++);
+ }
+ nRead++;
+ }
+ return nRead;
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package javajs.util;
+
+/**
+ * A class to insert a JavaScript debug statement for Firefox or Chrome debugger
+ *
+ */
+
+public class DebugJS {
+
+ /**
+ * Insert a JavaScript debug statement
+ *
+ */
+ public static void _(String msg) {
+ /**
+ * @j2sNative
+ *
+ * if (Clazz._debugging) {
+ *
+ * debugger;
+ *
+ * }
+ *
+ */
+ {}
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2005-11-10 09:52:44f -0600 (Thu, 10 Nov 2005) $
+ * $Revision: 4255 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.util;
+
+import javajs.api.EigenInterface;
+
+
+/**
+ * Eigenvalues and eigenvectors of a real matrix.
+ * See javajs.api.EigenInterface() as well.
+ *
+ * adapted by Bob Hanson from http://math.nist.gov/javanumerics/jama/ (public
+ * domain); adding quaternion superimposition capability; removing
+ * nonsymmetric reduction to Hessenberg form, which we do not need in Jmol.
+ *
+ * Output is as a set of double[n] columns, but for the EigenInterface
+ * we return them as V3[3] and float[3] (or double[3]) values.
+ *
+ * Eigenvalues and eigenvectors are sorted from smallest to largest eigenvalue.
+ *
+ * <P>
+ * If A is symmetric, then A = V*D*V' where the eigenvalue matrix D is diagonal
+ * and the eigenvector matrix V is orthogonal. I.e. A =
+ * V.times(D.times(V.transpose())) and V.times(V.transpose()) equals the
+ * identity matrix.
+ * <P>
+ * If A is not symmetric, then the eigenvalue matrix D is block diagonal with
+ * the real eigenvalues in 1-by-1 blocks and any complex eigenvalues, lambda +
+ * i*mu, in 2-by-2 blocks, [lambda, mu; -mu, lambda]. The columns of V represent
+ * the eigenvectors in the sense that A*V = V*D, i.e. A.times(V) equals
+ * V.times(D). The matrix V may be badly conditioned, or even singular, so the
+ * validity of the equation A = V*D*inverse(V) depends upon V.cond().
+ **/
+
+public class Eigen implements EigenInterface {
+
+ /* ------------------------
+ Public Methods
+ * ------------------------ */
+
+ public Eigen() {}
+
+ public Eigen set(int n) {
+ this.n = n;
+ V = new double[n][n];
+ d = new double[n];
+ e = new double[n];
+ return this;
+ }
+
+ @Override
+ public Eigen setM(double[][] m) {
+ set(m.length);
+ calc(m);
+ return this;
+ }
+
+ /**
+ * return values sorted from smallest to largest value.
+ */
+ @Override
+ public double[] getEigenvalues() {
+ return d;
+ }
+
+ /**
+ * Specifically for 3x3 systems, returns eigenVectors as V3[3]
+ * and values as float[3]; sorted from smallest to largest value.
+ *
+ * @param eigenVectors returned vectors
+ * @param eigenValues returned values
+ *
+ */
+ @Override
+ public void fillFloatArrays(V3[] eigenVectors, float[] eigenValues) {
+ for (int i = 0; i < 3; i++) {
+ if (eigenVectors != null) {
+ if (eigenVectors[i] == null)
+ eigenVectors[i] = new V3();
+ eigenVectors[i].set((float) V[0][i], (float) V[1][i], (float) V[2][i]);
+ }
+ if (eigenValues != null)
+ eigenValues[i] = (float) d[i];
+ }
+ }
+
+ /**
+ * Transpose V and turn into floats; sorted from smallest to largest value.
+ *
+ * @return ROWS of eigenvectors f[0], f[1], f[2], etc.
+ */
+ @Override
+ public float[][] getEigenvectorsFloatTransposed() {
+ float[][] f = new float[n][n];
+ for (int i = n; --i >= 0;)
+ for (int j = n; --j >= 0;)
+ f[j][i] = (float) V[i][j];
+ return f;
+ }
+
+
+ /**
+ * Check for symmetry, then construct the eigenvalue decomposition
+ *
+ * @param A
+ * Square matrix
+ */
+
+ public void calc(double[][] A) {
+
+ /* Jmol only has need of symmetric solutions
+ *
+ issymmetric = true;
+
+ for (int j = 0; (j < n) & issymmetric; j++) {
+ for (int i = 0; (i < n) & issymmetric; i++) {
+ issymmetric = (A[i][j] == A[j][i]);
+ }
+ }
+
+ if (issymmetric) {
+ */
+ for (int i = 0; i < n; i++) {
+ for (int j = 0; j < n; j++) {
+ V[i][j] = A[i][j];
+ }
+ }
+
+ // Tridiagonalize.
+ tred2();
+
+ // Diagonalize.
+ tql2();
+ /*
+ } else {
+ H = new double[n][n];
+ ort = new double[n];
+
+ for (int j = 0; j < n; j++) {
+ for (int i = 0; i < n; i++) {
+ H[i][j] = A[i][j];
+ }
+ }
+
+ // Reduce to Hessenberg form.
+ orthes();
+
+ // Reduce Hessenberg to real Schur form.
+ hqr2();
+ }
+ */
+
+ }
+
+ /**
+ * Return the real parts of the eigenvalues
+ *
+ * @return real(diag(D))
+ */
+
+ public double[] getRealEigenvalues() {
+ return d;
+ }
+
+ /**
+ * Return the imaginary parts of the eigenvalues
+ *
+ * @return imag(diag(D))
+ */
+
+ public double[] getImagEigenvalues() {
+ return e;
+ }
+
+ /* ------------------------
+ Class variables
+ * ------------------------ */
+
+ /**
+ * Row and column dimension (square matrix).
+ *
+ * @serial matrix dimension.
+ */
+ private int n = 3;
+
+ /**
+ * Symmetry flag.
+ *
+ * @serial internal symmetry flag.
+ */
+ //private boolean issymmetric = true;
+
+ /**
+ * Arrays for internal storage of eigenvalues.
+ *
+ * @serial internal storage of eigenvalues.
+ */
+ private double[] d, e;
+
+ /**
+ * Array for internal storage of eigenvectors.
+ *
+ * @serial internal storage of eigenvectors.
+ */
+ private double[][] V;
+
+ /**
+ * Array for internal storage of nonsymmetric Hessenberg form.
+ *
+ * @serial internal storage of nonsymmetric Hessenberg form.
+ */
+ //private double[][] H;
+
+ /**
+ * Working storage for nonsymmetric algorithm.
+ *
+ * @serial working storage for nonsymmetric algorithm.
+ */
+ //private double[] ort;
+
+ /* ------------------------
+ Private Methods
+ * ------------------------ */
+
+ // Symmetric Householder reduction to tridiagonal form.
+
+ private void tred2() {
+
+ // This is derived from the Algol procedures tred2 by
+ // Bowdler, Martin, Reinsch, and Wilkinson, Handbook for
+ // Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
+ // Fortran subroutine in EISPACK.
+
+ for (int j = 0; j < n; j++) {
+ d[j] = V[n - 1][j];
+ }
+
+ // Householder reduction to tridiagonal form.
+
+ for (int i = n - 1; i > 0; i--) {
+
+ // Scale to avoid under/overflow.
+
+ double scale = 0.0;
+ double h = 0.0;
+ for (int k = 0; k < i; k++) {
+ scale = scale + Math.abs(d[k]);
+ }
+ if (scale == 0.0) {
+ e[i] = d[i - 1];
+ for (int j = 0; j < i; j++) {
+ d[j] = V[i - 1][j];
+ V[i][j] = 0.0;
+ V[j][i] = 0.0;
+ }
+ } else {
+
+ // Generate Householder vector.
+
+ for (int k = 0; k < i; k++) {
+ d[k] /= scale;
+ h += d[k] * d[k];
+ }
+ double f = d[i - 1];
+ double g = Math.sqrt(h);
+ if (f > 0) {
+ g = -g;
+ }
+ e[i] = scale * g;
+ h = h - f * g;
+ d[i - 1] = f - g;
+ for (int j = 0; j < i; j++) {
+ e[j] = 0.0;
+ }
+
+ // Apply similarity transformation to remaining columns.
+
+ for (int j = 0; j < i; j++) {
+ f = d[j];
+ V[j][i] = f;
+ g = e[j] + V[j][j] * f;
+ for (int k = j + 1; k <= i - 1; k++) {
+ g += V[k][j] * d[k];
+ e[k] += V[k][j] * f;
+ }
+ e[j] = g;
+ }
+ f = 0.0;
+ for (int j = 0; j < i; j++) {
+ e[j] /= h;
+ f += e[j] * d[j];
+ }
+ double hh = f / (h + h);
+ for (int j = 0; j < i; j++) {
+ e[j] -= hh * d[j];
+ }
+ for (int j = 0; j < i; j++) {
+ f = d[j];
+ g = e[j];
+ for (int k = j; k <= i - 1; k++) {
+ V[k][j] -= (f * e[k] + g * d[k]);
+ }
+ d[j] = V[i - 1][j];
+ V[i][j] = 0.0;
+ }
+ }
+ d[i] = h;
+ }
+
+ // Accumulate transformations.
+
+ for (int i = 0; i < n - 1; i++) {
+ V[n - 1][i] = V[i][i];
+ V[i][i] = 1.0;
+ double h = d[i + 1];
+ if (h != 0.0) {
+ for (int k = 0; k <= i; k++) {
+ d[k] = V[k][i + 1] / h;
+ }
+ for (int j = 0; j <= i; j++) {
+ double g = 0.0;
+ for (int k = 0; k <= i; k++) {
+ g += V[k][i + 1] * V[k][j];
+ }
+ for (int k = 0; k <= i; k++) {
+ V[k][j] -= g * d[k];
+ }
+ }
+ }
+ for (int k = 0; k <= i; k++) {
+ V[k][i + 1] = 0.0;
+ }
+ }
+ for (int j = 0; j < n; j++) {
+ d[j] = V[n - 1][j];
+ V[n - 1][j] = 0.0;
+ }
+ V[n - 1][n - 1] = 1.0;
+ e[0] = 0.0;
+ }
+
+ // Symmetric tridiagonal QL algorithm.
+
+ private void tql2() {
+
+ // This is derived from the Algol procedures tql2, by
+ // Bowdler, Martin, Reinsch, and Wilkinson, Handbook for
+ // Auto. Comp., Vol.ii-Linear Algebra, and the corresponding
+ // Fortran subroutine in EISPACK.
+
+ for (int i = 1; i < n; i++) {
+ e[i - 1] = e[i];
+ }
+ e[n - 1] = 0.0;
+
+ double f = 0.0;
+ double tst1 = 0.0;
+ double eps = Math.pow(2.0, -52.0);
+ for (int l = 0; l < n; l++) {
+
+ // Find small subdiagonal element
+
+ tst1 = Math.max(tst1, Math.abs(d[l]) + Math.abs(e[l]));
+ int m = l;
+ while (m < n) {
+ if (Math.abs(e[m]) <= eps * tst1) {
+ break;
+ }
+ m++;
+ }
+
+ // If m == l, d[l] is an eigenvalue,
+ // otherwise, iterate.
+
+ if (m > l) {
+ int iter = 0;
+ do {
+ iter = iter + 1; // (Could check iteration count here.)
+
+ // Compute implicit shift
+
+ double g = d[l];
+ double p = (d[l + 1] - g) / (2.0 * e[l]);
+ double r = hypot(p, 1.0);
+ if (p < 0) {
+ r = -r;
+ }
+ d[l] = e[l] / (p + r);
+ d[l + 1] = e[l] * (p + r);
+ double dl1 = d[l + 1];
+ double h = g - d[l];
+ for (int i = l + 2; i < n; i++) {
+ d[i] -= h;
+ }
+ f = f + h;
+
+ // Implicit QL transformation.
+
+ p = d[m];
+ double c = 1.0;
+ double c2 = c;
+ double c3 = c;
+ double el1 = e[l + 1];
+ double s = 0.0;
+ double s2 = 0.0;
+ for (int i = m - 1; i >= l; i--) {
+ c3 = c2;
+ c2 = c;
+ s2 = s;
+ g = c * e[i];
+ h = c * p;
+ r = hypot(p, e[i]);
+ e[i + 1] = s * r;
+ s = e[i] / r;
+ c = p / r;
+ p = c * d[i] - s * g;
+ d[i + 1] = h + s * (c * g + s * d[i]);
+
+ // Accumulate transformation.
+
+ for (int k = 0; k < n; k++) {
+ h = V[k][i + 1];
+ V[k][i + 1] = s * V[k][i] + c * h;
+ V[k][i] = c * V[k][i] - s * h;
+ }
+ }
+ p = -s * s2 * c3 * el1 * e[l] / dl1;
+ e[l] = s * p;
+ d[l] = c * p;
+
+ // Check for convergence.
+
+ } while (Math.abs(e[l]) > eps * tst1);
+ }
+ d[l] = d[l] + f;
+ e[l] = 0.0;
+ }
+
+ // Sort eigenvalues and corresponding vectors.
+
+ for (int i = 0; i < n - 1; i++) {
+ int k = i;
+ double p = d[i];
+ for (int j = i + 1; j < n; j++) {
+ if (d[j] < p) {
+ k = j;
+ p = d[j];
+ }
+ }
+ if (k != i) {
+ d[k] = d[i];
+ d[i] = p;
+ for (int j = 0; j < n; j++) {
+ p = V[j][i];
+ V[j][i] = V[j][k];
+ V[j][k] = p;
+ }
+ }
+ }
+ }
+
+ private static double hypot(double a, double b) {
+
+ // sqrt(a^2 + b^2) without under/overflow.
+
+ double r;
+ if (Math.abs(a) > Math.abs(b)) {
+ r = b / a;
+ r = Math.abs(a) * Math.sqrt(1 + r * r);
+ } else if (b != 0) {
+ r = a / b;
+ r = Math.abs(b) * Math.sqrt(1 + r * r);
+ } else {
+ r = 0.0;
+ }
+ return r;
+ }
+
+ // Nonsymmetric reduction to Hessenberg form.
+
+ /*
+ private void orthes() {
+
+ // This is derived from the Algol procedures orthes and ortran,
+ // by Martin and Wilkinson, Handbook for Auto. Comp.,
+ // Vol.ii-Linear Algebra, and the corresponding
+ // Fortran subroutines in EISPACK.
+
+ int low = 0;
+ int high = n - 1;
+
+ for (int m = low + 1; m <= high - 1; m++) {
+
+ // Scale column.
+
+ double scale = 0.0;
+ for (int i = m; i <= high; i++) {
+ scale = scale + Math.abs(H[i][m - 1]);
+ }
+ if (scale != 0.0) {
+
+ // Compute Householder transformation.
+
+ double h = 0.0;
+ for (int i = high; i >= m; i--) {
+ ort[i] = H[i][m - 1] / scale;
+ h += ort[i] * ort[i];
+ }
+ double g = Math.sqrt(h);
+ if (ort[m] > 0) {
+ g = -g;
+ }
+ h = h - ort[m] * g;
+ ort[m] = ort[m] - g;
+
+ // Apply Householder similarity transformation
+ // H = (I-u*u'/h)*H*(I-u*u')/h)
+
+ for (int j = m; j < n; j++) {
+ double f = 0.0;
+ for (int i = high; i >= m; i--) {
+ f += ort[i] * H[i][j];
+ }
+ f = f / h;
+ for (int i = m; i <= high; i++) {
+ H[i][j] -= f * ort[i];
+ }
+ }
+
+ for (int i = 0; i <= high; i++) {
+ double f = 0.0;
+ for (int j = high; j >= m; j--) {
+ f += ort[j] * H[i][j];
+ }
+ f = f / h;
+ for (int j = m; j <= high; j++) {
+ H[i][j] -= f * ort[j];
+ }
+ }
+ ort[m] = scale * ort[m];
+ H[m][m - 1] = scale * g;
+ }
+ }
+
+ // Accumulate transformations (Algol's ortran).
+
+ for (int i = 0; i < n; i++) {
+ for (int j = 0; j < n; j++) {
+ V[i][j] = (i == j ? 1.0 : 0.0);
+ }
+ }
+
+ for (int m = high - 1; m >= low + 1; m--) {
+ if (H[m][m - 1] != 0.0) {
+ for (int i = m + 1; i <= high; i++) {
+ ort[i] = H[i][m - 1];
+ }
+ for (int j = m; j <= high; j++) {
+ double g = 0.0;
+ for (int i = m; i <= high; i++) {
+ g += ort[i] * V[i][j];
+ }
+ // Double division avoids possible underflow
+ g = (g / ort[m]) / H[m][m - 1];
+ for (int i = m; i <= high; i++) {
+ V[i][j] += g * ort[i];
+ }
+ }
+ }
+ }
+ }
+
+ // Complex scalar division.
+
+ private transient double cdivr, cdivi;
+
+ private void cdiv(double xr, double xi, double yr, double yi) {
+ double r, d;
+ if (Math.abs(yr) > Math.abs(yi)) {
+ r = yi / yr;
+ d = yr + r * yi;
+ cdivr = (xr + r * xi) / d;
+ cdivi = (xi - r * xr) / d;
+ } else {
+ r = yr / yi;
+ d = yi + r * yr;
+ cdivr = (r * xr + xi) / d;
+ cdivi = (r * xi - xr) / d;
+ }
+ }
+
+ // Nonsymmetric reduction from Hessenberg to real Schur form.
+
+ private void hqr2() {
+
+ // This is derived from the Algol procedure hqr2,
+ // by Martin and Wilkinson, Handbook for Auto. Comp.,
+ // Vol.ii-Linear Algebra, and the corresponding
+ // Fortran subroutine in EISPACK.
+
+ // Initialize
+
+ int nn = this.n;
+ int n = nn - 1;
+ int low = 0;
+ int high = nn - 1;
+ double eps = Math.pow(2.0, -52.0);
+ double exshift = 0.0;
+ double p = 0, q = 0, r = 0, s = 0, z = 0, t, w, x, y;
+
+ // Store roots isolated by balanc and compute matrix norm
+
+ double norm = 0.0;
+ for (int i = 0; i < nn; i++) {
+ if (i < low || i > high) {
+ d[i] = H[i][i];
+ e[i] = 0.0;
+ }
+ for (int j = Math.max(i - 1, 0); j < nn; j++) {
+ norm = norm + Math.abs(H[i][j]);
+ }
+ }
+
+ // Outer loop over eigenvalue index
+
+ int iter = 0;
+ while (n >= low) {
+
+ // Look for single small sub-diagonal element
+
+ int l = n;
+ while (l > low) {
+ s = Math.abs(H[l - 1][l - 1]) + Math.abs(H[l][l]);
+ if (s == 0.0) {
+ s = norm;
+ }
+ if (Math.abs(H[l][l - 1]) < eps * s) {
+ break;
+ }
+ l--;
+ }
+
+ // Check for convergence
+ // One root found
+
+ if (l == n) {
+ H[n][n] = H[n][n] + exshift;
+ d[n] = H[n][n];
+ e[n] = 0.0;
+ n--;
+ iter = 0;
+
+ // Two roots found
+
+ } else if (l == n - 1) {
+ w = H[n][n - 1] * H[n - 1][n];
+ p = (H[n - 1][n - 1] - H[n][n]) / 2.0;
+ q = p * p + w;
+ z = Math.sqrt(Math.abs(q));
+ H[n][n] = H[n][n] + exshift;
+ H[n - 1][n - 1] = H[n - 1][n - 1] + exshift;
+ x = H[n][n];
+
+ // Real pair
+
+ if (q >= 0) {
+ if (p >= 0) {
+ z = p + z;
+ } else {
+ z = p - z;
+ }
+ d[n - 1] = x + z;
+ d[n] = d[n - 1];
+ if (z != 0.0) {
+ d[n] = x - w / z;
+ }
+ e[n - 1] = 0.0;
+ e[n] = 0.0;
+ x = H[n][n - 1];
+ s = Math.abs(x) + Math.abs(z);
+ p = x / s;
+ q = z / s;
+ r = Math.sqrt(p * p + q * q);
+ p = p / r;
+ q = q / r;
+
+ // Row modification
+
+ for (int j = n - 1; j < nn; j++) {
+ z = H[n - 1][j];
+ H[n - 1][j] = q * z + p * H[n][j];
+ H[n][j] = q * H[n][j] - p * z;
+ }
+
+ // Column modification
+
+ for (int i = 0; i <= n; i++) {
+ z = H[i][n - 1];
+ H[i][n - 1] = q * z + p * H[i][n];
+ H[i][n] = q * H[i][n] - p * z;
+ }
+
+ // Accumulate transformations
+
+ for (int i = low; i <= high; i++) {
+ z = V[i][n - 1];
+ V[i][n - 1] = q * z + p * V[i][n];
+ V[i][n] = q * V[i][n] - p * z;
+ }
+
+ // Complex pair
+
+ } else {
+ d[n - 1] = x + p;
+ d[n] = x + p;
+ e[n - 1] = z;
+ e[n] = -z;
+ }
+ n = n - 2;
+ iter = 0;
+
+ // No convergence yet
+
+ } else {
+
+ // Form shift
+
+ x = H[n][n];
+ y = 0.0;
+ w = 0.0;
+ if (l < n) {
+ y = H[n - 1][n - 1];
+ w = H[n][n - 1] * H[n - 1][n];
+ }
+
+ // Wilkinson's original ad hoc shift
+
+ if (iter == 10) {
+ exshift += x;
+ for (int i = low; i <= n; i++) {
+ H[i][i] -= x;
+ }
+ s = Math.abs(H[n][n - 1]) + Math.abs(H[n - 1][n - 2]);
+ x = y = 0.75 * s;
+ w = -0.4375 * s * s;
+ }
+
+ // MATLAB's new ad hoc shift
+
+ if (iter == 30) {
+ s = (y - x) / 2.0;
+ s = s * s + w;
+ if (s > 0) {
+ s = Math.sqrt(s);
+ if (y < x) {
+ s = -s;
+ }
+ s = x - w / ((y - x) / 2.0 + s);
+ for (int i = low; i <= n; i++) {
+ H[i][i] -= s;
+ }
+ exshift += s;
+ x = y = w = 0.964;
+ }
+ }
+
+ iter = iter + 1; // (Could check iteration count here.)
+
+ // Look for two consecutive small sub-diagonal elements
+
+ int m = n - 2;
+ while (m >= l) {
+ z = H[m][m];
+ r = x - z;
+ s = y - z;
+ p = (r * s - w) / H[m + 1][m] + H[m][m + 1];
+ q = H[m + 1][m + 1] - z - r - s;
+ r = H[m + 2][m + 1];
+ s = Math.abs(p) + Math.abs(q) + Math.abs(r);
+ p = p / s;
+ q = q / s;
+ r = r / s;
+ if (m == l) {
+ break;
+ }
+ if (Math.abs(H[m][m - 1]) * (Math.abs(q) + Math.abs(r)) < eps
+ * (Math.abs(p) * (Math.abs(H[m - 1][m - 1]) + Math.abs(z) + Math
+ .abs(H[m + 1][m + 1])))) {
+ break;
+ }
+ m--;
+ }
+
+ for (int i = m + 2; i <= n; i++) {
+ H[i][i - 2] = 0.0;
+ if (i > m + 2) {
+ H[i][i - 3] = 0.0;
+ }
+ }
+
+ // Double QR step involving rows l:n and columns m:n
+
+ for (int k = m; k <= n - 1; k++) {
+ boolean notlast = (k != n - 1);
+ if (k != m) {
+ p = H[k][k - 1];
+ q = H[k + 1][k - 1];
+ r = (notlast ? H[k + 2][k - 1] : 0.0);
+ x = Math.abs(p) + Math.abs(q) + Math.abs(r);
+ if (x != 0.0) {
+ p = p / x;
+ q = q / x;
+ r = r / x;
+ }
+ }
+ if (x == 0.0) {
+ break;
+ }
+ s = Math.sqrt(p * p + q * q + r * r);
+ if (p < 0) {
+ s = -s;
+ }
+ if (s != 0) {
+ if (k != m) {
+ H[k][k - 1] = -s * x;
+ } else if (l != m) {
+ H[k][k - 1] = -H[k][k - 1];
+ }
+ p = p + s;
+ x = p / s;
+ y = q / s;
+ z = r / s;
+ q = q / p;
+ r = r / p;
+
+ // Row modification
+
+ for (int j = k; j < nn; j++) {
+ p = H[k][j] + q * H[k + 1][j];
+ if (notlast) {
+ p = p + r * H[k + 2][j];
+ H[k + 2][j] = H[k + 2][j] - p * z;
+ }
+ H[k][j] = H[k][j] - p * x;
+ H[k + 1][j] = H[k + 1][j] - p * y;
+ }
+
+ // Column modification
+
+ for (int i = 0; i <= Math.min(n, k + 3); i++) {
+ p = x * H[i][k] + y * H[i][k + 1];
+ if (notlast) {
+ p = p + z * H[i][k + 2];
+ H[i][k + 2] = H[i][k + 2] - p * r;
+ }
+ H[i][k] = H[i][k] - p;
+ H[i][k + 1] = H[i][k + 1] - p * q;
+ }
+
+ // Accumulate transformations
+
+ for (int i = low; i <= high; i++) {
+ p = x * V[i][k] + y * V[i][k + 1];
+ if (notlast) {
+ p = p + z * V[i][k + 2];
+ V[i][k + 2] = V[i][k + 2] - p * r;
+ }
+ V[i][k] = V[i][k] - p;
+ V[i][k + 1] = V[i][k + 1] - p * q;
+ }
+ } // (s != 0)
+ } // k loop
+ } // check convergence
+ } // while (n >= low)
+
+ // Backsubstitute to find vectors of upper triangular form
+
+ if (norm == 0.0) {
+ return;
+ }
+
+ for (n = nn - 1; n >= 0; n--) {
+ p = d[n];
+ q = e[n];
+
+ // Real vector
+
+ if (q == 0) {
+ int l = n;
+ H[n][n] = 1.0;
+ for (int i = n - 1; i >= 0; i--) {
+ w = H[i][i] - p;
+ r = 0.0;
+ for (int j = l; j <= n; j++) {
+ r = r + H[i][j] * H[j][n];
+ }
+ if (e[i] < 0.0) {
+ z = w;
+ s = r;
+ } else {
+ l = i;
+ if (e[i] == 0.0) {
+ if (w != 0.0) {
+ H[i][n] = -r / w;
+ } else {
+ H[i][n] = -r / (eps * norm);
+ }
+
+ // Solve real equations
+
+ } else {
+ x = H[i][i + 1];
+ y = H[i + 1][i];
+ q = (d[i] - p) * (d[i] - p) + e[i] * e[i];
+ t = (x * s - z * r) / q;
+ H[i][n] = t;
+ if (Math.abs(x) > Math.abs(z)) {
+ H[i + 1][n] = (-r - w * t) / x;
+ } else {
+ H[i + 1][n] = (-s - y * t) / z;
+ }
+ }
+
+ // Overflow control
+
+ t = Math.abs(H[i][n]);
+ if ((eps * t) * t > 1) {
+ for (int j = i; j <= n; j++) {
+ H[j][n] = H[j][n] / t;
+ }
+ }
+ }
+ }
+
+ // Complex vector
+
+ } else if (q < 0) {
+ int l = n - 1;
+
+ // Last vector component imaginary so matrix is triangular
+
+ if (Math.abs(H[n][n - 1]) > Math.abs(H[n - 1][n])) {
+ H[n - 1][n - 1] = q / H[n][n - 1];
+ H[n - 1][n] = -(H[n][n] - p) / H[n][n - 1];
+ } else {
+ cdiv(0.0, -H[n - 1][n], H[n - 1][n - 1] - p, q);
+ H[n - 1][n - 1] = cdivr;
+ H[n - 1][n] = cdivi;
+ }
+ H[n][n - 1] = 0.0;
+ H[n][n] = 1.0;
+ for (int i = n - 2; i >= 0; i--) {
+ double ra, sa, vr, vi;
+ ra = 0.0;
+ sa = 0.0;
+ for (int j = l; j <= n; j++) {
+ ra = ra + H[i][j] * H[j][n - 1];
+ sa = sa + H[i][j] * H[j][n];
+ }
+ w = H[i][i] - p;
+
+ if (e[i] < 0.0) {
+ z = w;
+ r = ra;
+ s = sa;
+ } else {
+ l = i;
+ if (e[i] == 0) {
+ cdiv(-ra, -sa, w, q);
+ H[i][n - 1] = cdivr;
+ H[i][n] = cdivi;
+ } else {
+
+ // Solve complex equations
+
+ x = H[i][i + 1];
+ y = H[i + 1][i];
+ vr = (d[i] - p) * (d[i] - p) + e[i] * e[i] - q * q;
+ vi = (d[i] - p) * 2.0 * q;
+ if (vr == 0.0 & vi == 0.0) {
+ vr = eps
+ * norm
+ * (Math.abs(w) + Math.abs(q) + Math.abs(x) + Math.abs(y) + Math
+ .abs(z));
+ }
+ cdiv(x * r - z * ra + q * sa, x * s - z * sa - q * ra, vr, vi);
+ H[i][n - 1] = cdivr;
+ H[i][n] = cdivi;
+ if (Math.abs(x) > (Math.abs(z) + Math.abs(q))) {
+ H[i + 1][n - 1] = (-ra - w * H[i][n - 1] + q * H[i][n]) / x;
+ H[i + 1][n] = (-sa - w * H[i][n] - q * H[i][n - 1]) / x;
+ } else {
+ cdiv(-r - y * H[i][n - 1], -s - y * H[i][n], z, q);
+ H[i + 1][n - 1] = cdivr;
+ H[i + 1][n] = cdivi;
+ }
+ }
+
+ // Overflow control
+
+ t = Math.max(Math.abs(H[i][n - 1]), Math.abs(H[i][n]));
+ if ((eps * t) * t > 1) {
+ for (int j = i; j <= n; j++) {
+ H[j][n - 1] = H[j][n - 1] / t;
+ H[j][n] = H[j][n] / t;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ // Vectors of isolated roots
+
+ for (int i = 0; i < nn; i++) {
+ if (i < low || i > high) {
+ for (int j = i; j < nn; j++) {
+ V[i][j] = H[i][j];
+ }
+ }
+ }
+
+ // Back transformation to get eigenvectors of original matrix
+
+ for (int j = nn - 1; j >= low; j--) {
+ for (int i = low; i <= high; i++) {
+ z = 0.0;
+ for (int k = low; k <= Math.min(j, high); k++) {
+ z = z + V[i][k] * H[k][j];
+ }
+ V[i][j] = z;
+ }
+ }
+ }
+ */
+
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2011 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package javajs.util;
+
+public enum Encoding {
+ NONE, UTF8, UTF_16BE, UTF_16LE, UTF_32BE, UTF_32LE
+}
\ No newline at end of file
--- /dev/null
+package javajs.util;
+
+import javax.sound.sampled.AudioFormat;
+import javax.sound.sampled.AudioSystem;
+import javax.sound.sampled.DataLine;
+import javax.sound.sampled.SourceDataLine;
+
+import sun.audio.AudioData;
+import sun.audio.AudioDataStream;
+import sun.audio.AudioPlayer;
+
+
+/**
+ * The JSAudioThread adds a layer to JSThread that is specific for audio.
+ * This class utilizes JSAudioLine, which is not fully fleshed out.
+ *
+ * Two very simple interfaces,
+ *
+ * (new JSAudioThread()).playULawData(byte[] b);
+ *
+ * and
+ *
+ * (new JSAudioThread(audioFormat)).playOnce(byte[] b, offset, length);
+ *
+ * allow straightforward audio production without having to work with
+ * SourceDataLine directly.
+ *
+ * As a JSThread, this class implements myInit(), isLooping(), myLoop(),
+ * whenDone(), onException(), and doFinally().
+ *
+ * If the constructor JSAudioThread(JSAudioThreadUser, AudioFormat, byte[]) is
+ * used, then the JSAudioThreadUser must simply implement fillAudioBuffer(),
+ * checkSoundStatus(), and audioThreadExiting() for very simple streaming audio.
+ * JSAudioThread will then take care of all the timing issues.
+ *
+ * But the implementer is welcome to override any of the JSThread overrides
+ * themselves in order to customize this further.
+ *
+ * The standard streaming case, then is:
+ *
+ * audioThread = new JSAudioThread(audioUser, audioFormat, audioByteBuffer);
+ * audioThread.start();
+ *
+ * where audioUser provides
+ *
+ * checkSoundStatus() (called in isLooping()),
+ *
+ * fillAudioBuffer() (called in myLoop()),
+ *
+ * and
+ *
+ * audioThreadExiting() (called in doFinally()).
+ *
+ * @author Bob Hanson
+ *
+ */
+public class JSAudioThread extends JSThread {
+
+ protected Owner owner;
+ protected boolean done;
+ protected int myBufferLength;
+ protected SourceDataLine line;
+ protected int rate, nChannels, bitsPerSample;
+
+ protected byte[] audioByteBuffer;
+ protected int audioBufferByteLength;
+
+ private AudioFormat audioFormat;
+ private int myBufferOffset;
+ private int playCount;
+
+ public JSAudioThread(Owner owner, AudioFormat audioFormat, byte[] audioByteBuffer) {
+ this.owner = owner;
+ setFormat(audioFormat);
+ setBuffer(audioByteBuffer);
+ }
+
+ /**
+ * A convenience constructor requiring standard settings of
+ * signed (for 8-bit) and littleEndian (for 16-bit)
+ *
+ * @param owner
+ * @param rate
+ * @param bitsPerSample
+ * @param nChannels
+ * @param audioByteBuffer
+ */
+ public JSAudioThread(Owner owner, int rate, int bitsPerSample, int nChannels, byte[] audioByteBuffer) {
+ this.owner = owner;
+ setFormat(new AudioFormat(rate, bitsPerSample, nChannels, true, false));
+ setBuffer(audioByteBuffer);
+ }
+
+ /**
+ * primarily available for (new JSAudioThread()).playULawData
+ *
+ */
+ public JSAudioThread() {
+ }
+
+ /**
+ * primarily available for (new JSAudioThread()).playOnce
+ *
+ */
+ public JSAudioThread(AudioFormat audioFormat) {
+ setFormat(audioFormat);
+ }
+
+ /**
+ *
+ * A simple 8-bit uLaw data player
+ *
+ * @param data
+ */
+ public void playULawData(byte[] data) {
+ // this constructor uses default new AudioFormat(ULAW,8000,8,1,1,8000,true)
+ // threading is taken care of by the browser in JavaScript
+ AudioPlayer.player.start(new AudioDataStream(new AudioData(data)));
+ }
+
+
+ /**
+ * Just play once through; no additions
+ *
+ * @param data
+ */
+ public void playOnce(byte[] data, int offset, int length) {
+ setBuffer(data);
+ myBufferOffset = offset;
+ myBufferLength = length;
+ playCount = 1;
+ start();
+ }
+
+ public void setBuffer(byte[] audioByteBuffer) {
+ this.audioByteBuffer = audioByteBuffer;
+ audioBufferByteLength = audioByteBuffer.length;
+ }
+
+ public SourceDataLine getLine() {
+ return line;
+ }
+
+ public AudioFormat getFormat() {
+ return audioFormat;
+ }
+
+ public void setFormat(AudioFormat audioFormat) {
+ this.audioFormat = audioFormat;
+ rate = (int) audioFormat.getSampleRate();
+ bitsPerSample = audioFormat.getSampleSizeInBits();
+ nChannels = audioFormat.getChannels();
+ }
+
+ public void resetAudio() {
+ if (line == null)
+ return;
+ line.flush();
+ line.close();
+ line = null;
+ }
+
+ /**
+ * Standard initialization of a SourceDataLine
+ *
+ */
+ @Override
+ protected boolean myInit() {
+ try {
+ DataLine.Info info = new DataLine.Info(SourceDataLine.class, audioFormat);
+ if (line != null)
+ line.close();
+ line = (SourceDataLine) AudioSystem.getLine(info);
+ line.open(audioFormat, audioBufferByteLength);
+ line.start();
+ } catch (Exception e) {
+ e.printStackTrace();
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ protected boolean isLooping() {
+ return !done && (--playCount >= 0 || owner != null && owner.checkSoundStatus());
+ }
+
+ @Override
+ protected boolean myLoop() {
+ if (!done) {
+ if ((myBufferLength = (owner == null ? myBufferLength : owner.fillAudioBuffer())) <= 0)
+ return !(done = true);
+ try {
+ if (line == null)
+ myInit();
+ line.write(audioByteBuffer, myBufferOffset, myBufferLength);
+ } catch (Exception e) {
+ e.printStackTrace();
+ done = true;
+ }
+ }
+ return !done;
+ }
+
+ @Override
+ protected void whenDone() {
+ done = true;
+ resetAudio();
+ }
+
+ @Override
+ protected int getDelayMillis() {
+ // about 25% of the actual play time
+ return 1000 // ms/sec
+ * (myBufferLength * 8 / bitsPerSample) // * samples
+ / rate // * seconds/sample)
+ / nChannels // / number of channels
+ / 4; // * 25%
+ }
+
+ @Override
+ protected void onException(Exception e) {
+ e.printStackTrace();
+ }
+
+ @Override
+ protected void doFinally() {
+ if (owner != null)
+ owner.audioThreadExiting();
+ }
+
+ public interface Owner {
+
+ /**
+ *
+ * @return true if thread should continue; false if not
+ *
+ */
+ boolean checkSoundStatus();
+
+ /** fill audio buffer
+ *
+ * @return number of bytes to write to audio line
+ *
+ */
+ int fillAudioBuffer();
+
+ /**
+ * called from the finally clause when complete
+ *
+ */
+ void audioThreadExiting();
+
+
+ }
+
+}
+
--- /dev/null
+package javajs.util;
+
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.J2SIgnoreImport;
+
+
+
+/**
+ * a very simple JSON parser for JSON objects that are compatible with JavaScript
+ * A gross simplification of https://github.com/douglascrockford/JSON-java
+ *
+ * A SUBSET of JSON with similarly to window.JSON.parse():
+ *
+ * In JavaScript returns "null" for a null value, not null
+ *
+ * -- requires quoted strings for keys and values
+ *
+ * -- does not allow /xxx/ objects
+ *
+ * @author Bob Hanson
+ *
+ */
+@J2SIgnoreImport({ HashMap.class })
+public class JSJSONParser {
+
+ private String str;
+ private int index;
+ private int len;
+ private boolean asHashTable;
+
+ public JSJSONParser () {
+ // for reflection
+ }
+
+ /**
+ * requires { "key":"value", "key":"value",....}
+ *
+ * @param str
+ * @param asHashTable TODO
+ *
+ * @return Map or null
+ */
+ @SuppressWarnings("unchecked")
+ public Map<String, Object> parseMap(String str, boolean asHashTable) {
+ index = 0;
+ this.asHashTable = asHashTable;
+ this.str = str;
+ len = str.length();
+ if (getChar() != '{')
+ return null;
+ returnChar();
+ return (Map<String, Object>) getValue(false);
+ }
+
+ /**
+ * Could return Integer, Float, Boolean, String, Map<String, Object>, Lst<Object>, or null
+ *
+ * @param str
+ * @return a object equivalent to the JSON string str
+ *
+ */
+ public Object parse(String str) {
+ index = 0;
+ this.str = str;
+ len = str.length();
+ return getValue(false);
+ }
+
+ private char next() {
+ return (index < len ? str.charAt(index++) : '\0');
+ }
+
+ private void returnChar() {
+ index--;
+ }
+
+ /**
+ * Get the next char in the string, skipping whitespace.
+ *
+ * @throws JSONException
+ * @return one character, or 0 if there are no more characters.
+ */
+ private char getChar() throws JSONException {
+ for (;;) {
+ char c = next();
+ if (c == 0 || c > ' ') {
+ return c;
+ }
+ }
+ }
+
+ /**
+ * only allowing the following values:
+ *
+ * {...} object
+ *
+ * [...] array
+ *
+ * Integer
+ *
+ * Float
+ *
+ * "quoted string"
+ *
+ *
+ * @param isKey if we should allow {...} and [...]
+ * @return a subclass of Object
+ * @throws JSONException
+ */
+ private Object getValue(boolean isKey) throws JSONException {
+ int i = index;
+ char c = getChar();
+ switch (c) {
+ case '\0':
+ return null;
+ case '"':
+ case '\'':
+ return getString(c);
+ case '{':
+ if (!isKey)
+ return getObject();
+ c = 0;
+ break;
+ case '[':
+ if (!isKey)
+ return getArray();
+ c = 0;
+ break;
+ default:
+ // standard syntax is assumed; not checking all possible invalid keys
+ // for example, "-" is not allowed in JavaScript, which is what this is for
+ returnChar();
+ while (c >= ' ' && "[,]{:}'\"".indexOf(c) < 0)
+ c = next();
+ returnChar();
+ if (isKey && c != ':')
+ c = 0;
+ break;
+ }
+ if (isKey && c == 0)
+ throw new JSONException("invalid key");
+
+ String string = str.substring(i, index);
+
+ // check for the only valid simple words: true, false, null (lower case)
+ // and in this case, only for
+
+ if (!isKey) {
+ if (string.equals("true")) {
+ return Boolean.TRUE;
+ }
+ if (string.equals("false")) {
+ return Boolean.FALSE;
+ }
+ if (string.equals("null")) {
+ return (asHashTable ? string : null);
+ }
+ }
+ // only numbers from here on:
+
+ c = string.charAt(0);
+ if (c >= '0' && c <= '9' || c == '-')
+ try {
+ if (string.indexOf('.') < 0 && string.indexOf('e') < 0
+ && string.indexOf('E') < 0)
+ return new Integer(string);
+ // not allowing infinity or NaN
+ // using float here because Jmol does not use Double
+ Float d = Float.valueOf(string);
+ if (!d.isInfinite() && !d.isNaN())
+ return d;
+ } catch (Exception e) {
+ }
+ // not a valid number
+ System.out.println("JSON parser cannot parse " + string);
+ throw new JSONException("invalid value");
+ }
+
+ private String getString(char quote) throws JSONException {
+ char c;
+ SB sb = null;
+ int i0 = index;
+ for (;;) {
+ int i1 = index;
+ switch (c = next()) {
+ case '\0':
+ case '\n':
+ case '\r':
+ throw syntaxError("Unterminated string");
+ case '\\':
+ switch (c = next()) {
+ case '"':
+ case '\'':
+ case '\\':
+ case '/':
+ break;
+ case 'b':
+ c = '\b';
+ break;
+ case 't':
+ c = '\t';
+ break;
+ case 'n':
+ c = '\n';
+ break;
+ case 'f':
+ c = '\f';
+ break;
+ case 'r':
+ c = '\r';
+ break;
+ case 'u':
+ int i = index;
+ index += 4;
+ try {
+ c = (char) Integer.parseInt(str.substring(i, index), 16);
+ } catch (Exception e) {
+ throw syntaxError("Substring bounds error");
+ }
+ break;
+ default:
+ throw syntaxError("Illegal escape.");
+ }
+ break;
+ default:
+ if (c == quote)
+ return (sb == null ? str.substring(i0, i1) : sb.toString());
+ break;
+ }
+ if (index > i1 + 1) {
+ if (sb == null) {
+ sb = new SB();
+ sb.append(str.substring(i0, i1));
+ }
+ }
+ if (sb != null)
+ sb.appendC(c);
+ }
+ }
+
+ private Object getObject() {
+ Map<String, Object> map = (asHashTable ? new Hashtable<String, Object>() : new HashMap<String, Object>());
+ String key = null;
+ switch (getChar()) {
+ case '}':
+ return map;
+ case 0:
+ throw new JSONException("invalid object");
+ }
+ returnChar();
+ boolean isKey = false;
+ for (;;) {
+ if ((isKey = !isKey) == true)
+ key = getValue(true).toString();
+ else
+ map.put(key, getValue(false));
+ switch (getChar()) {
+ case '}':
+ return map;
+ case ':':
+ if (isKey)
+ continue;
+ isKey = true;
+ //$FALL-THROUGH$
+ case ',':
+ if (!isKey)
+ continue;
+ //$FALL-THROUGH$
+ default:
+ throw syntaxError("Expected ',' or ':' or '}'");
+ }
+ }
+ }
+
+ private Object getArray() {
+ Lst<Object> l = new Lst<Object>();
+ switch (getChar()) {
+ case ']':
+ return l;
+ case 0:
+ throw new JSONException("invalid array");
+ }
+ returnChar();
+ boolean isNull = false;
+ for (;;) {
+ if (isNull) {
+ l.addLast(null);
+ isNull = false;
+ } else {
+ l.addLast(getValue(false));
+ }
+ switch (getChar()) {
+ case ',':
+ switch (getChar()) {
+ case ']':
+ // terminal ,
+ return l;
+ case ',':
+ // empty value
+ isNull = true;
+ //$FALL-THROUGH$
+ default:
+ returnChar();
+ }
+ continue;
+ case ']':
+ return l;
+ default:
+ throw syntaxError("Expected ',' or ']'");
+ }
+ }
+ }
+
+ /**
+ * Make a JSONException to signal a syntax error.
+ *
+ * @param message
+ * The error message.
+ * @return A JSONException object, suitable for throwing
+ */
+ public JSONException syntaxError(String message) {
+ return new JSONException(message + " for " + str.substring(0, Math.min(index, len)));
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+public class JSONException extends RuntimeException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public JSONException(String message) {
+ super(message);
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+import java.awt.Toolkit;
+import java.awt.event.InvocationEvent;
+
+//import javajs.J2SRequireImport;
+import javajs.api.JSFunction;
+
+
+/**
+ * An abstract class that takes care of simple threading in Java or JavaScript.
+ *
+ * To use it, subclass it and complete the necessary methods.
+ *
+ *
+ * There are three states: INIT, LOOP, and DONE.
+ *
+ * These states are passed into run1
+ *
+ *
+ * @author Bob Hanson
+ *
+ */
+//@J2SRequireImport(swingjs.JSToolkit.class)
+public abstract class JSThread extends Thread implements JSFunction {
+
+ public static final int INIT = 0;
+ public static final int LOOP = 1;
+ public static final int DONE = 2;
+
+ public static int threadCount = 0;
+
+ protected boolean isJS;
+
+ public JSThread() {
+ this(null, "JSThread-" + (++threadCount));
+ }
+
+ public JSThread(String name) {
+ this(null, name);
+ }
+
+ public JSThread(ThreadGroup group, String name) {
+ super(group, name);
+ /**
+ * @j2sNative
+ *
+ * this.isJS = true;
+ */
+ {}
+ }
+
+ @Override
+ public void run() {
+ run1(INIT);
+ }
+
+ @Override
+ public synchronized void start() {
+
+
+ /**
+ * @j2sNative
+ *
+ * Clazz.load("swingjs.JSToolkit").dispatch$O$I$I(this, 1, 0);
+ *
+ */
+ {
+ super.start();
+ }
+
+ }
+
+ /**
+ * thread initialization
+ *
+ * @return false to exit thread before any looping
+ */
+ protected abstract boolean myInit();
+
+ /**
+ * check for continuing to loop
+ *
+ * @return true if we are to continue looping
+ */
+ protected abstract boolean isLooping();
+
+ /**
+ *
+ * @return false to handle sleepAndReturn yourself
+ */
+ protected abstract boolean myLoop();
+ /**
+ * what to do when the DONE state is reached
+ *
+ */
+ protected abstract void whenDone();
+
+ /**
+ *
+ * @return the sleep time in milliseconds
+ */
+ protected abstract int getDelayMillis();
+
+ /**
+ * handle an exception -- state will be set to DONE no matter what you do here
+ *
+ * @param e
+ */
+ protected abstract void onException(Exception e);
+
+ /**
+ * anything you want done in try{}catch(}finally().
+ * Note that this method is not fired if we are in JavaScript
+ * mode and the normal return from sleepAndReturn() is taken.
+ *
+ */
+ protected abstract void doFinally();
+
+ /**
+ * a generic method that loops until done, either in Java or JavaScript.
+ *
+ * In JavaScript it will reenter and continue at the appropriate spot.
+ *
+ * This method may be overridden if desired.
+ *
+ * @see org.uwi.SimThread
+ *
+ * @param state
+ */
+ protected void run1(int state) {
+ boolean executeFinally = true;
+ // called by thisThread.run();
+ try {
+ while (!interrupted()) {
+ switch (state) {
+ case INIT:
+ if (!myInit())
+ return;
+ // initial code here
+ state = LOOP;
+ continue;
+ case LOOP:
+ // to stop looping, return false from isLooping()
+ if (!isLooping()) {
+ state = DONE;
+ continue;
+ }
+ // To handle sleepAndReturn yourself, or to skip the
+ // sleep when desired, return false from myLoop();
+ // Note that doFinally must not be executed in this case.
+ // This is because JavaScript will do a return here
+ // for every loop, and Java will not.
+ if (myLoop() && sleepAndReturn(getDelayMillis(), state)) {
+ executeFinally = false;
+ return;
+ }
+ continue;
+ case DONE:
+ whenDone();
+ // whatever
+ return;
+ }
+ }
+ } catch (Exception e) {
+ onException(e);
+ state = DONE;
+ } finally {
+ if (executeFinally)
+ doFinally();
+ }
+ // normal exit
+ }
+
+ /**
+ *
+ * @param r2
+ * @param state
+ * @return true if we should interrupt (i.e. JavaScript)
+ * @throws InterruptedException
+ */
+ protected boolean sleepAndReturn(final int delay, final int state)
+ throws InterruptedException {
+ if (!isJS) {
+ sleep(delay);
+ return false;
+ }
+
+ // in JavaScript, we need to do this through the system event queue,
+ // which in JSToolkit takes care of all the "thread" handling.
+
+ final JSThread me = this;
+ Runnable r = new Runnable() {
+ @Override
+ public void run() {
+ me.run1(state);
+ }
+ };
+ /**
+ * @j2sNative
+ *
+ * setTimeout(
+ * function() {java.awt.Toolkit.getDefaultToolkit().getSystemEventQueue().postEvent$java_awt_AWTEvent(Clazz.new(java.awt.event.InvocationEvent.c$$O$Runnable,[me, r]))},
+ * delay);
+ *
+ */
+ {
+ Toolkit.getDefaultToolkit().getSystemEventQueue()
+ .postEvent(new InvocationEvent(me, r));
+ }
+ return true;
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+import java.io.BufferedReader;
+
+/**
+ * A simple class to read a designated number of bytes from a
+ * file and then return them line by line, skipping lines that
+ * start with #, and including the \n or \r characters at line ends.
+ *
+ * Generally useful for determining what sort of data a file contains.
+ *
+ */
+public class LimitedLineReader {
+ private char[] buf;
+ private int cchBuf;
+ private int ichCurrent;
+
+ public LimitedLineReader(BufferedReader bufferedReader, int readLimit)
+ throws Exception {
+ bufferedReader.mark(readLimit + 1);
+ buf = new char[readLimit];
+ cchBuf = Math.max(bufferedReader.read(buf, 0, readLimit), 0);
+ ichCurrent = 0;
+ bufferedReader.reset();
+ }
+
+ public String getHeader(int n) {
+ return (n == 0 ? new String(buf) : new String(buf, 0, Math.min(cchBuf, n)));
+ }
+
+ public String readLineWithNewline() {
+ while (ichCurrent < cchBuf) {
+ int ichBeginningOfLine = ichCurrent;
+ char ch = 0;
+ while (ichCurrent < cchBuf &&
+ (ch = buf[ichCurrent++]) != '\r' && ch != '\n') {
+ }
+ if (ch == '\r' && ichCurrent < cchBuf && buf[ichCurrent] == '\n')
+ ++ichCurrent;
+ int cchLine = ichCurrent - ichBeginningOfLine;
+ if (buf[ichBeginningOfLine] == '#')
+ continue; // flush comment lines;
+ return new String(buf, ichBeginningOfLine, cchLine);
+ }
+ return "";
+ }
+}
+
--- /dev/null
+package javajs.util;
+
+import java.io.IOException;
+
+
+
+
+
+/**
+ *
+ * VectorDataReader subclasses BufferedReader and overrides its
+ * read, readLine, mark, and reset methods so that JmolAdapter
+ * works with Vector<String> arrays without any further adaptation.
+ *
+ */
+
+public class ListDataReader extends DataReader {
+ private Lst<String> data;
+ private int pt;
+ private int len;
+
+ public ListDataReader() {
+ super();
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public DataReader setData(Object data) {
+ this.data = (Lst<String>) data;
+ len = this.data.size();
+ return this;
+ }
+
+ @Override
+ public int read(char[] buf, int off, int len) throws IOException {
+ return readBuf(buf, off, len);
+ }
+
+ @Override
+ public String readLine() {
+ return (pt < len ? data.get(pt++) : null);
+ }
+
+ /**
+ *
+ * @param ptr
+ */
+ public void mark(long ptr) {
+ //ignore ptr.
+ ptMark = pt;
+ }
+
+ @Override
+ public void reset() {
+ pt = ptMark;
+ }
+}
\ No newline at end of file
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-04-26 16:57:51 -0500 (Thu, 26 Apr 2007) $
+ * $Revision: 7502 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.util;
+
+import java.util.ArrayList;
+
+/**
+ * created to remove ambiguities in add and remove
+ *
+ * @param <V>
+ */
+@SuppressWarnings("serial")
+public class Lst<V> extends ArrayList<V> {
+
+ public Lst() {
+ super();
+ }
+
+ public boolean addLast(V v) {
+ return super.add(v);
+ }
+
+ public V removeItemAt(int location) {
+ return super.remove(location);
+ }
+
+ public boolean removeObj(Object v) {
+ return super.remove(v);
+ }
+
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+import java.io.Serializable;
+
+
+
+/**
+ * A single precision floating point 3 by 3 matrix.
+ *
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012 for unique
+ * constructor and method names for the optimization of compiled
+ * JavaScript using Java2Script.
+ *
+ *
+ *
+ */
+@SuppressWarnings("serial")
+public class M3 extends M34 implements Serializable {
+
+ /**
+ * Constructs and initializes a Matrix3f from the specified 9 element array.
+ * this.m00 =v[0], this.m01=v[1], etc.
+ *
+ * @param v
+ * the array of length 9 containing in order
+ * @return m
+ */
+ public static M3 newA9(float[] v) {
+ M3 m = new M3();
+ m.setA(v);
+ return m;
+ }
+
+ /**
+ * Constructs a new matrix with the same values as the Matrix3f parameter.
+ *
+ * @param m1
+ * The source matrix.
+ * @return m
+ */
+ public static M3 newM3(M3 m1) {
+ M3 m = new M3();
+ if (m1 == null) {
+ m.setScale(1);
+ return m;
+ }
+ m.m00 = m1.m00;
+ m.m01 = m1.m01;
+ m.m02 = m1.m02;
+
+ m.m10 = m1.m10;
+ m.m11 = m1.m11;
+ m.m12 = m1.m12;
+
+ m.m20 = m1.m20;
+ m.m21 = m1.m21;
+ m.m22 = m1.m22;
+ return m;
+ }
+
+ /**
+ * Sets this Matrix3f to a scalar * Identity.
+ * @param scale
+ */
+ public void setScale(float scale) {
+ clear33();
+ m00 = m11 = m22 = scale;
+ }
+
+ /**
+ * Sets the value of this matrix to the double value of the Matrix3f argument.
+ *
+ * @param m1
+ * the matrix3f
+ */
+ public void setM3(M34 m1) {
+ setM33(m1);
+ }
+ /**
+ * Sets the values in this Matrix3f equal to the row-major array parameter
+ * (ie, the first four elements of the array will be copied into the first row
+ * of this matrix, etc.).
+ *
+ * @param m
+ */
+ public void setA(float m[]) {
+ m00 = m[0];
+ m01 = m[1];
+ m02 = m[2];
+ m10 = m[3];
+ m11 = m[4];
+ m12 = m[5];
+ m20 = m[6];
+ m21 = m[7];
+ m22 = m[8];
+ }
+
+ /**
+ * Sets the specified element of this matrix3d to the value provided.
+ *
+ * @param row
+ * the row number to be modified (zero indexed)
+ * @param col
+ * the column number to be modified (zero indexed)
+ * @param v
+ * the new value
+ */
+ public void setElement(int row, int col, float v) {
+ set33(row, col, v);
+ }
+
+ /**
+ * Retrieves the value at the specified row and column of this matrix.
+ *
+ * @param row
+ * the row number to be retrieved (zero indexed)
+ * @param col
+ * the column number to be retrieved (zero indexed)
+ * @return the value at the indexed element
+ */
+ public float getElement(int row, int col) {
+ return get33(row, col);
+ }
+
+ /**
+ * Sets the specified row of this matrix3d to the three values provided.
+ *
+ * @param row
+ * the row number to be modified (zero indexed)
+ * @param x
+ * the first column element
+ * @param y
+ * the second column element
+ * @param z
+ * the third column element
+ */
+ public void setRow(int row, float x, float y, float z) {
+ switch (row) {
+ case 0:
+ m00 = x;
+ m01 = y;
+ m02 = z;
+ return;
+ case 1:
+ m10 = x;
+ m11 = y;
+ m12 = z;
+ return;
+ case 2:
+ m20 = x;
+ m21 = y;
+ m22 = z;
+ return;
+ default:
+ err();
+ }
+ }
+
+ /**
+ * Sets the specified row of this matrix3d to the Vector provided.
+ *
+ * @param row
+ * the row number to be modified (zero indexed)
+ * @param v
+ * the replacement row
+ */
+ public void setRowV(int row, T3 v) {
+ switch (row) {
+ case 0:
+ m00 = v.x;
+ m01 = v.y;
+ m02 = v.z;
+ return;
+ case 1:
+ m10 = v.x;
+ m11 = v.y;
+ m12 = v.z;
+ return;
+ case 2:
+ m20 = v.x;
+ m21 = v.y;
+ m22 = v.z;
+ return;
+ default:
+ err();
+ }
+ }
+
+ /**
+ * Sets the specified row of this matrix3d to the four values provided.
+ *
+ * @param row
+ * the row number to be modified (zero indexed)
+ * @param v
+ * the replacement row
+ */
+ public void setRowA(int row, float v[]) {
+ setRow33(row, v);
+ }
+
+ /**
+ * Copies the matrix values in the specified row into the array parameter.
+ *
+ * @param row
+ * the matrix row
+ * @param v
+ * The array into which the matrix row values will be copied
+ */
+ @Override
+ public void getRow(int row, float v[]) {
+ getRow33(row, v);
+ }
+
+ /**
+ * Sets the specified column of this matrix3d to the three values provided.
+ *
+ * @param column
+ * the column number to be modified (zero indexed)
+ * @param x
+ * the first row element
+ * @param y
+ * the second row element
+ * @param z
+ * the third row element
+ */
+ public void setColumn3(int column, float x, float y, float z) {
+ switch (column) {
+ case 0:
+ m00 = x;
+ m10 = y;
+ m20 = z;
+ break;
+ case 1:
+ m01 = x;
+ m11 = y;
+ m21 = z;
+ break;
+ case 2:
+ m02 = x;
+ m12 = y;
+ m22 = z;
+ break;
+ default:
+ err();
+ }
+ }
+
+ /**
+ * Sets the specified column of this matrix3d to the vector provided.
+ *
+ * @param column
+ * the column number to be modified (zero indexed)
+ * @param v
+ * the replacement column
+ */
+ public void setColumnV(int column, T3 v) {
+ switch (column) {
+ case 0:
+ m00 = v.x;
+ m10 = v.y;
+ m20 = v.z;
+ break;
+ case 1:
+ m01 = v.x;
+ m11 = v.y;
+ m21 = v.z;
+ break;
+ case 2:
+ m02 = v.x;
+ m12 = v.y;
+ m22 = v.z;
+ break;
+ default:
+ err();
+ }
+ }
+
+ /**
+ * Copies the matrix values in the specified column into the vector parameter.
+ *
+ * @param column
+ * the matrix column
+ * @param v
+ * The vector into which the matrix row values will be copied
+ */
+ public void getColumnV(int column, T3 v) {
+ switch (column) {
+ case 0:
+ v.x = m00;
+ v.y = m10;
+ v.z = m20;
+ break;
+ case 1:
+ v.x = m01;
+ v.y = m11;
+ v.z = m21;
+ break;
+ case 2:
+ v.x = m02;
+ v.y = m12;
+ v.z = m22;
+ break;
+ default:
+ err();
+ }
+ }
+
+ /**
+ * Sets the specified column of this matrix3d to the four values provided.
+ *
+ * @param column
+ * the column number to be modified (zero indexed)
+ * @param v
+ * the replacement column
+ */
+ public void setColumnA(int column, float v[]) {
+ setColumn33(column, v);
+ }
+
+ /**
+ * Copies the matrix values in the specified column into the array parameter.
+ *
+ * @param column
+ * the matrix column
+ * @param v
+ * The array into which the matrix row values will be copied
+ */
+ public void getColumn(int column, float v[]) {
+ getColumn33(column, v);
+ }
+
+ /**
+ * Sets the value of this matrix to sum of itself and matrix m1.
+ *
+ * @param m1
+ * the other matrix
+ */
+ public void add(M3 m1) {
+ add33(m1);
+ }
+
+ /**
+ * Sets the value of this matrix to the matrix difference of itself and matrix
+ * m1 (this = this - m1).
+ *
+ * @param m1
+ * the other matrix
+ */
+ public void sub(M3 m1) {
+ sub33(m1);
+ }
+
+ /**
+ * Sets the value of this matrix to its transpose.
+ */
+ public void transpose() {
+ transpose33();
+ }
+
+ /**
+ * Sets the value of this matrix to the transpose of the argument matrix
+ *
+ * @param m1
+ * the matrix to be transposed
+ */
+ public void transposeM(M3 m1) {
+ // alias-safe
+ setM33(m1);
+ transpose33();
+ }
+
+ /**
+ * Sets the value of this matrix to the matrix inverse of the passed matrix
+ * m1.
+ *
+ * @param m1
+ * the matrix to be inverted
+ */
+ public void invertM(M3 m1) {
+ setM33(m1);
+ invert();
+ }
+
+ /**
+ * Sets the value of this matrix to its inverse.
+ */
+ public void invert() {
+ double s = determinant3();
+ if (s == 0.0)
+ return;
+ s = 1 / s;
+ // alias-safe way.
+ set9(m11 * m22 - m12 * m21, m02 * m21 - m01 * m22, m01 * m12 - m02 * m11,
+ m12 * m20 - m10 * m22, m00 * m22 - m02 * m20, m02 * m10 - m00 * m12,
+ m10 * m21 - m11 * m20, m01 * m20 - m00 * m21, m00 * m11 - m01 * m10);
+ scale((float) s);
+ }
+
+ /**
+ * Sets the value of this matrix to a rotation matrix about the x axis by the
+ * passed angle.
+ *
+ * @param angle
+ * the angle to rotate about the X axis in radians
+ * @return this
+ */
+ public M3 setAsXRotation(float angle) {
+ setXRot(angle);
+ return this;
+ }
+
+ /**
+ * Sets the value of this matrix to a rotation matrix about the y axis by the
+ * passed angle.
+ *
+ * @param angle
+ * the angle to rotate about the Y axis in radians
+ * @return this
+ */
+ public M3 setAsYRotation(float angle) {
+ setYRot(angle);
+ return this;
+ }
+
+ /**
+ * Sets the value of this matrix to a rotation matrix about the z axis by the
+ * passed angle.
+ *
+ * @param angle
+ * the angle to rotate about the Z axis in radians
+ * @return this
+ */
+ public M3 setAsZRotation(float angle) {
+ setZRot(angle);
+ return this;
+ }
+
+ /**
+ * Multiplies each element of this matrix by a scalar.
+ *
+ * @param scalar
+ * The scalar multiplier.
+ */
+ public void scale(float scalar) {
+ mul33(scalar);
+ }
+
+ /**
+ * Sets the value of this matrix to the result of multiplying itself with
+ * matrix m1.
+ *
+ * @param m1
+ * the other matrix
+ */
+ public void mul(M3 m1) {
+ mul2(this, m1);
+ }
+
+ /**
+ * Sets the value of this matrix to the result of multiplying the two argument
+ * matrices together.
+ *
+ * @param m1
+ * the first matrix
+ * @param m2
+ * the second matrix
+ */
+ public void mul2(M3 m1, M3 m2) {
+ // alias-safe way.
+ set9(m1.m00 * m2.m00 + m1.m01 * m2.m10 + m1.m02 * m2.m20, m1.m00 * m2.m01
+ + m1.m01 * m2.m11 + m1.m02 * m2.m21, m1.m00 * m2.m02 + m1.m01 * m2.m12
+ + m1.m02 * m2.m22,
+
+ m1.m10 * m2.m00 + m1.m11 * m2.m10 + m1.m12 * m2.m20, m1.m10 * m2.m01
+ + m1.m11 * m2.m11 + m1.m12 * m2.m21, m1.m10 * m2.m02 + m1.m11 * m2.m12
+ + m1.m12 * m2.m22,
+
+ m1.m20 * m2.m00 + m1.m21 * m2.m10 + m1.m22 * m2.m20, m1.m20 * m2.m01
+ + m1.m21 * m2.m11 + m1.m22 * m2.m21, m1.m20 * m2.m02 + m1.m21 * m2.m12
+ + m1.m22 * m2.m22);
+ }
+
+ /**
+ * Returns true if the Object o is of type Matrix3f and all of the data
+ * members of t1 are equal to the corresponding data members in this Matrix3f.
+ *
+ * @param o
+ * the object with which the comparison is made.
+ */
+ @Override
+ public boolean equals(Object o) {
+ if (!(o instanceof M3))
+ return false;
+ M3 m = (M3) o;
+ return m00 == m.m00 && m01 == m.m01 && m02 == m.m02 && m10 == m.m10
+ && m11 == m.m11 && m12 == m.m12 && m20 == m.m20 && m21 == m.m21
+ && m22 == m.m22;
+ }
+
+ /**
+ * Returns a hash number based on the data values in this object. Two
+ * different Matrix3f objects with identical data values (ie, returns true for
+ * equals(Matrix3f) ) will return the same hash number. Two objects with
+ * different data members may return the same hash value, although this is not
+ * likely.
+ *
+ * @return the integer hash value
+ */
+ @Override
+ public int hashCode() {
+ return T3.floatToIntBits(m00) ^ T3.floatToIntBits(m01)
+ ^ T3.floatToIntBits(m02) ^ T3.floatToIntBits(m10)
+ ^ T3.floatToIntBits(m11) ^ T3.floatToIntBits(m12)
+ ^ T3.floatToIntBits(m20) ^ T3.floatToIntBits(m21)
+ ^ T3.floatToIntBits(m22);
+ }
+
+ /**
+ * Sets this matrix to all zeros.
+ */
+ public void setZero() {
+ clear33();
+ }
+
+ /**
+ * Sets 9 values
+ *
+ * @param m00
+ * @param m01
+ * @param m02
+ * @param m10
+ * @param m11
+ * @param m12
+ * @param m20
+ * @param m21
+ * @param m22
+ */
+ private void set9(float m00, float m01, float m02, float m10, float m11,
+ float m12, float m20, float m21, float m22) {
+ this.m00 = m00;
+ this.m01 = m01;
+ this.m02 = m02;
+ this.m10 = m10;
+ this.m11 = m11;
+ this.m12 = m12;
+ this.m20 = m20;
+ this.m21 = m21;
+ this.m22 = m22;
+ }
+
+ /**
+ * Returns a string that contains the values of this Matrix3f.
+ *
+ * @return the String representation
+ */
+ @Override
+ public String toString() {
+ return "[\n [" + m00 + "\t" + m01 + "\t" + m02 + "]" + "\n [" + m10
+ + "\t" + m11 + "\t" + m12 + "]" + "\n [" + m20 + "\t" + m21 + "\t"
+ + m22 + "] ]";
+ }
+
+ /**
+ * Sets the value of this matrix to the matrix conversion of the single
+ * precision axis and angle argument.
+ *
+ * @param a
+ * the axis and angle to be converted
+ * @return this
+ */
+ public M3 setAA(A4 a) {
+ setAA33(a);
+ return this;
+ }
+
+ /**
+ * 3D ball rotation from dx dy in-plane mouse motion
+ * adapted from Andrew Hanson
+ * Computer Graphics beyond the Third Dimension:
+ * Geometry, Orientation Control, and Rendering for
+ * Graphics in Dimensions Greater than Three
+ * Course Notes for SIGGRAPH ’98
+ * http://www.cse.ohio-state.edu/~hwshen/888_su02/hanson_note.pdf
+ *
+ * @param responseFactor Jmol uses 0.02 here
+ * @param dx
+ * @param dy
+ * @return true if successful; false if not;
+ */
+ public boolean setAsBallRotation(float responseFactor, float dx, float dy) {
+ float r = (float) Math.sqrt(dx * dx + dy * dy);
+ float th = r * responseFactor;
+ if (th == 0) {
+ setScale(1);
+ return false;
+ }
+ float c = (float) Math.cos(th);
+ float s = (float) Math.sin(th);
+ float nx = -dy / r;
+ float ny = dx / r;
+ float c1 = c - 1;
+ m00 = 1 + c1 * nx * nx;
+ m01 = m10 = c1 * nx * ny;
+ m20 = -(m02 = s * nx);
+ m11 = 1 + c1 * ny * ny;
+ m21 = -(m12 = s * ny);
+ m22 = c;
+ return true;
+ }
+
+ public boolean isRotation() {
+ return (Math.abs(determinant3() - 1) < 0.001f);
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+/**
+ * A base class for both M3 and M4 to conserve code size.
+ *
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012 for unique
+ * constructor and method names for the optimization of compiled
+ * JavaScript using Java2Script.
+ * and for subclassing to M3 and M4
+ *
+ */
+public abstract class M34 {
+
+ /**
+ * The first element of the first row
+ */
+ public float m00;
+
+ /**
+ * The second element of the first row.
+ */
+ public float m01;
+
+ /**
+ * third element of the first row.
+ */
+ public float m02;
+
+ /**
+ * The first element of the second row.
+ */
+ public float m10;
+
+ /**
+ * The second element of the second row.
+ */
+ public float m11;
+
+ /**
+ * The third element of the second row.
+ */
+ public float m12;
+
+ /**
+ * The first element of the third row.
+ */
+ public float m20;
+
+ /**
+ * The second element of the third row.
+ */
+ public float m21;
+
+ /**
+ * The third element of the third row.
+ */
+ public float m22;
+
+ protected void setAA33(A4 a) {
+ double x = a.x;
+ double y = a.y;
+ double z = a.z;
+ double angle = a.angle;
+ // Taken from Rick's which is taken from Wertz. pg. 412
+ // Bug Fixed and changed into right-handed by hiranabe
+ double n = Math.sqrt(x * x + y * y + z * z);
+ // zero-div may occur
+ n = 1 / n;
+ x *= n;
+ y *= n;
+ z *= n;
+ double c = Math.cos(angle);
+ double s = Math.sin(angle);
+ double omc = 1.0 - c;
+ m00 = (float) (c + x * x * omc);
+ m11 = (float) (c + y * y * omc);
+ m22 = (float) (c + z * z * omc);
+
+ double tmp1 = x * y * omc;
+ double tmp2 = z * s;
+ m01 = (float) (tmp1 - tmp2);
+ m10 = (float) (tmp1 + tmp2);
+
+ tmp1 = x * z * omc;
+ tmp2 = y * s;
+ m02 = (float) (tmp1 + tmp2);
+ m20 = (float) (tmp1 - tmp2);
+
+ tmp1 = y * z * omc;
+ tmp2 = x * s;
+ m12 = (float) (tmp1 - tmp2);
+ m21 = (float) (tmp1 + tmp2);
+ }
+
+ public void rotate(T3 t) {
+ // alias-safe
+ rotate2(t, t);
+ }
+
+ /**
+ * Transform the vector vec using this Matrix3f and place the result into
+ * vecOut.
+ *
+ * @param t
+ * the single precision vector to be transformed
+ * @param result
+ * the vector into which the transformed values are placed
+ */
+ public void rotate2(T3 t, T3 result) {
+ // alias-safe
+ result.set(m00 * t.x + m01 * t.y + m02 * t.z, m10 * t.x + m11 * t.y + m12
+ * t.z, m20 * t.x + m21 * t.y + m22 * t.z);
+ }
+
+
+ /**
+ * Sets the value of this matrix to the double value of the Matrix3f argument.
+ *
+ * @param m1
+ * the matrix3f
+ */
+ protected void setM33(M34 m1) {
+ m00 = m1.m00;
+ m01 = m1.m01;
+ m02 = m1.m02;
+ m10 = m1.m10;
+ m11 = m1.m11;
+ m12 = m1.m12;
+ m20 = m1.m20;
+ m21 = m1.m21;
+ m22 = m1.m22;
+ }
+
+ protected void clear33() {
+ m00 = m01 = m02 = m10 = m11 = m12 = m20 = m21 = m22 = 0.0f;
+ }
+
+ protected void set33(int row, int col, float v) {
+ switch (row) {
+ case 0:
+ switch (col) {
+ case 0:
+ m00 = v;
+ return;
+ case 1:
+ m01 = v;
+ return;
+ case 2:
+ m02 = v;
+ return;
+ }
+ break;
+ case 1:
+ switch (col) {
+ case 0:
+ m10 = v;
+ return;
+ case 1:
+ m11 = v;
+ return;
+ case 2:
+ m12 = v;
+ return;
+ }
+ break;
+ case 2:
+ switch (col) {
+ case 0:
+ m20 = v;
+ return;
+ case 1:
+ m21 = v;
+ return;
+ case 2:
+ m22 = v;
+ return;
+ }
+ break;
+ }
+ err();
+ }
+
+ protected float get33(int row, int col) {
+ switch (row) {
+ case 0:
+ switch (col) {
+ case 0:
+ return m00;
+ case 1:
+ return m01;
+ case 2:
+ return m02;
+ }
+ break;
+ case 1:
+ switch (col) {
+ case 0:
+ return m10;
+ case 1:
+ return m11;
+ case 2:
+ return m12;
+ }
+ break;
+ case 2:
+ switch (col) {
+ case 0:
+ return m20;
+ case 1:
+ return m21;
+ case 2:
+ return m22;
+ }
+ break;
+ }
+ err();
+ return 0;
+ }
+
+ protected void setRow33(int row, float v[]) {
+ switch (row) {
+ case 0:
+ m00 = v[0];
+ m01 = v[1];
+ m02 = v[2];
+ return;
+ case 1:
+ m10 = v[0];
+ m11 = v[1];
+ m12 = v[2];
+ return;
+ case 2:
+ m20 = v[0];
+ m21 = v[1];
+ m22 = v[2];
+ return;
+ default:
+ err();
+ }
+ }
+
+ public abstract void getRow(int row, float v[]);
+
+ protected void getRow33(int row, float v[]) {
+ switch (row) {
+ case 0:
+ v[0] = m00;
+ v[1] = m01;
+ v[2] = m02;
+ return;
+ case 1:
+ v[0] = m10;
+ v[1] = m11;
+ v[2] = m12;
+ return;
+ case 2:
+ v[0] = m20;
+ v[1] = m21;
+ v[2] = m22;
+ return;
+ }
+ err();
+ }
+
+ protected void setColumn33(int column, float v[]) {
+ switch(column) {
+ case 0:
+ m00 = v[0];
+ m10 = v[1];
+ m20 = v[2];
+ break;
+ case 1:
+ m01 = v[0];
+ m11 = v[1];
+ m21 = v[2];
+ break;
+ case 2:
+ m02 = v[0];
+ m12 = v[1];
+ m22 = v[2];
+ break;
+ default:
+ err();
+ }
+ }
+
+ protected void getColumn33(int column, float v[]) {
+ switch(column) {
+ case 0:
+ v[0] = m00;
+ v[1] = m10;
+ v[2] = m20;
+ break;
+ case 1:
+ v[0] = m01;
+ v[1] = m11;
+ v[2] = m21;
+ break;
+ case 2:
+ v[0] = m02;
+ v[1] = m12;
+ v[2] = m22;
+ break;
+ default:
+ err();
+ }
+ }
+
+ protected void add33(M34 m1) {
+ m00 += m1.m00;
+ m01 += m1.m01;
+ m02 += m1.m02;
+ m10 += m1.m10;
+ m11 += m1.m11;
+ m12 += m1.m12;
+ m20 += m1.m20;
+ m21 += m1.m21;
+ m22 += m1.m22;
+ }
+
+ protected void sub33(M34 m1) {
+ m00 -= m1.m00;
+ m01 -= m1.m01;
+ m02 -= m1.m02;
+ m10 -= m1.m10;
+ m11 -= m1.m11;
+ m12 -= m1.m12;
+ m20 -= m1.m20;
+ m21 -= m1.m21;
+ m22 -= m1.m22;
+ }
+
+ protected void mul33(float x) {
+ m00 *= x;
+ m01 *= x;
+ m02 *= x;
+ m10 *= x;
+ m11 *= x;
+ m12 *= x;
+ m20 *= x;
+ m21 *= x;
+ m22 *= x;
+ }
+
+ protected void transpose33() {
+ float tmp = m01;
+ m01 = m10;
+ m10 = tmp;
+
+ tmp = m02;
+ m02 = m20;
+ m20 = tmp;
+
+ tmp = m12;
+ m12 = m21;
+ m21 = tmp;
+ }
+
+ protected void setXRot(float angle) {
+ double c = Math.cos(angle);
+ double s = Math.sin(angle);
+ m00 = 1.0f;
+ m01 = 0.0f;
+ m02 = 0.0f;
+ m10 = 0.0f;
+ m11 = (float) c;
+ m12 = (float) -s;
+ m20 = 0.0f;
+ m21 = (float) s;
+ m22 = (float) c;
+ }
+
+ protected void setYRot(float angle) {
+ double c = Math.cos(angle);
+ double s = Math.sin(angle);
+ m00 = (float) c;
+ m01 = 0.0f;
+ m02 = (float) s;
+ m10 = 0.0f;
+ m11 = 1.0f;
+ m12 = 0.0f;
+ m20 = (float) -s;
+ m21 = 0.0f;
+ m22 = (float) c;
+ }
+
+ protected void setZRot(float angle) {
+ double c = Math.cos(angle);
+ double s = Math.sin(angle);
+ m00 = (float) c;
+ m01 = (float) -s;
+ m02 = 0.0f;
+ m10 = (float) s;
+ m11 = (float) c;
+ m12 = 0.0f;
+ m20 = 0.0f;
+ m21 = 0.0f;
+ m22 = 1.0f;
+ }
+
+ /**
+ * @return 3x3 determinant
+ */
+ public float determinant3() {
+ return m00 * (m11 * m22 - m21 * m12) - m01 * (m10 * m22 - m20 * m12) + m02
+ * (m10 * m21 - m20 * m11);
+ }
+
+ protected void err() {
+ throw new ArrayIndexOutOfBoundsException(
+ "matrix column/row out of bounds");
+ }
+
+
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+/**
+ * A single precision floating point 4 by 4 matrix.
+ *
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012 for unique
+ * constructor and method names for the optimization of compiled
+ * JavaScript using Java2Script.
+ *
+ */
+public class M4 extends M34 {
+
+ /**
+ * The fourth element of the first row.
+ */
+ public float m03;
+
+ /**
+ * The fourth element of the second row.
+ */
+ public float m13;
+
+ /**
+ * The fourth element of the third row.
+ */
+ public float m23;
+
+ /**
+ * The first element of the fourth row.
+ */
+ public float m30;
+
+ /**
+ * The second element of the fourth row.
+ */
+ public float m31;
+
+ /**
+ * The third element of the fourth row.
+ */
+ public float m32;
+
+ /**
+ * The fourth element of the fourth row.
+ */
+ public float m33 = 0;
+
+ public M4() {
+ }
+ /**
+ * Constructs and initializes a Matrix4f from the specified 16 element array.
+ * this.m00 =v[0], this.m01=v[1], etc.
+ *
+ * @param v
+ * the array of length 16 containing in order
+ * @return m
+ */
+ public static M4 newA16(float[] v) {
+ M4 m = new M4();
+ m.m00 = v[0];
+ m.m01 = v[1];
+ m.m02 = v[2];
+ m.m03 = v[3];
+
+ m.m10 = v[4];
+ m.m11 = v[5];
+ m.m12 = v[6];
+ m.m13 = v[7];
+
+ m.m20 = v[8];
+ m.m21 = v[9];
+ m.m22 = v[10];
+ m.m23 = v[11];
+
+ m.m30 = v[12];
+ m.m31 = v[13];
+ m.m32 = v[14];
+ m.m33 = v[15];
+
+ return m;
+ }
+
+ /**
+ * Constructs a new matrix with the same values as the Matrix4f parameter.
+ *
+ * @param m1
+ * the source matrix
+ * @return m
+ */
+ public static M4 newM4(M4 m1) {
+ M4 m = new M4();
+ if (m1 == null) {
+ m.setIdentity();
+ return m;
+ }
+ m.setToM3(m1);
+ m.m03 = m1.m03;
+ m.m13 = m1.m13;
+ m.m23 = m1.m23;
+ m.m30 = m1.m30;
+ m.m31 = m1.m31;
+ m.m32 = m1.m32;
+ m.m33 = m1.m33;
+ return m;
+ }
+
+ /**
+ * Constructs and initializes a Matrix4f from the rotation matrix and
+ * translation.
+ *
+ * @param m1
+ * The rotation matrix representing the rotational components
+ * @param t
+ * The translational components of the matrix
+ * @return m
+ */
+ public static M4 newMV(M3 m1, T3 t) {
+ M4 m = new M4();
+ m.setMV(m1, t);
+ return m;
+ }
+
+ /**
+ * Sets this matrix to all zeros.
+ */
+ public void setZero() {
+ clear33();
+ m03 = m13 = m23 = m30 = m31 = m32 = m33 = 0.0f;
+ }
+
+ /**
+ * Sets this Matrix4f to identity.
+ */
+ public void setIdentity() {
+ setZero();
+ m00 = m11 = m22 = m33 = 1.0f;
+ }
+
+ /**
+ * Sets the value of this matrix to a copy of the passed matrix m1.
+ *
+ * @param m1
+ * the matrix to be copied
+ * @return this
+ */
+ public M4 setM4(M4 m1) {
+ setM33(m1);
+ m03 = m1.m03;
+ m13 = m1.m13;
+ m23 = m1.m23;
+ m30 = m1.m30;
+ m31 = m1.m31;
+ m32 = m1.m32;
+ m33 = m1.m33;
+ return this;
+ }
+
+ /**
+ * Initializes a Matrix4f from the rotation matrix and translation.
+ *
+ * @param m1
+ * The rotation matrix representing the rotational components
+ * @param t
+ * The translational components of the matrix
+ */
+ public void setMV(M3 m1, T3 t) {
+ setM33(m1);
+ setTranslation(t);
+ m33 = 1;
+ }
+
+ /**
+ * Sets the rotational component (upper 3x3) of this matrix to the matrix
+ * values in the single precision Matrix3f argument; the other elements of
+ * this matrix are initialized as if this were an identity matrix (ie, affine
+ * matrix with no translational component).
+ *
+ * @param m1
+ * the 3x3 matrix
+ */
+ public void setToM3(M34 m1) {
+ setM33(m1);
+ m03 = m13 = m23 = m30 = m31 = m32 = 0.0f;
+ m33 = 1.0f;
+ }
+
+ /**
+ * Sets the rotational component (upper 3x3) of this matrix
+ * to a rotation given by an axis angle
+ *
+ * @param a
+ * the axis and angle to be converted
+ */
+ public void setToAA(A4 a) {
+ setIdentity();
+ setAA33(a);
+ }
+
+ /**
+ * Sets the values in this Matrix4f equal to the row-major array parameter
+ * (ie, the first four elements of the array will be copied into the first row
+ * of this matrix, etc.).
+ *
+ * @param m
+ */
+ public void setA(float m[]) {
+ m00 = m[0];
+ m01 = m[1];
+ m02 = m[2];
+ m03 = m[3];
+ m10 = m[4];
+ m11 = m[5];
+ m12 = m[6];
+ m13 = m[7];
+ m20 = m[8];
+ m21 = m[9];
+ m22 = m[10];
+ m23 = m[11];
+ m30 = m[12];
+ m31 = m[13];
+ m32 = m[14];
+ m33 = m[15];
+ }
+
+ /**
+ * Modifies the translational components of this matrix to the values of the
+ * Vector3f argument; the other values of this matrix are not modified.
+ *
+ * @param trans
+ * the translational component
+ */
+ public void setTranslation(T3 trans) {
+ m03 = trans.x;
+ m13 = trans.y;
+ m23 = trans.z;
+ }
+
+ /**
+ * Sets the specified element of this matrix4f to the value provided.
+ *
+ * @param row
+ * the row number to be modified (zero indexed)
+ * @param col
+ * the column number to be modified (zero indexed)
+ * @param v
+ * the new value
+ */
+ public void setElement(int row, int col, float v) {
+ if (row < 3 && col < 3) {
+ set33(row, col, v);
+ return;
+ }
+ if (row > 3 || col > 3)
+ err();
+ switch (row) {
+ case 0:
+ m03 = v;
+ return;
+ case 1:
+ m13 = v;
+ return;
+ case 2:
+ m23 = v;
+ return;
+ }
+ switch (col) {
+ case 0:
+ m30 = v;
+ return;
+ case 1:
+ m31 = v;
+ return;
+ case 2:
+ m32 = v;
+ return;
+ case 3:
+ m33 = v;
+ return;
+ }
+ }
+
+ /**
+ * Retrieves the value at the specified row and column of this matrix.
+ *
+ * @param row
+ * the row number to be retrieved (zero indexed)
+ * @param col
+ * the column number to be retrieved (zero indexed)
+ * @return the value at the indexed element
+ */
+ public float getElement(int row, int col) {
+ if (row < 3 && col < 3)
+ return get33(row, col);
+ if (row > 3 || col > 3) {
+ err();
+ return 0;
+ }
+ switch (row) {
+ case 0:
+ return m03;
+ case 1:
+ return m13;
+ case 2:
+ return m23;
+ default:
+ switch (col) {
+ case 0:
+ return m30;
+ case 1:
+ return m31;
+ case 2:
+ return m32;
+ default:
+ return m33;
+ }
+ }
+ }
+
+ /**
+ * Retrieves the translational components of this matrix.
+ *
+ * @param trans
+ * the vector that will receive the translational component
+ */
+ public void getTranslation(T3 trans) {
+ trans.x = m03;
+ trans.y = m13;
+ trans.z = m23;
+ }
+
+ /**
+ * Gets the upper 3x3 values of this matrix and places them into the matrix
+ * m1.
+ *
+ * @param m1
+ * The matrix that will hold the values
+ */
+ public void getRotationScale(M3 m1) {
+ m1.m00 = m00;
+ m1.m01 = m01;
+ m1.m02 = m02;
+ m1.m10 = m10;
+ m1.m11 = m11;
+ m1.m12 = m12;
+ m1.m20 = m20;
+ m1.m21 = m21;
+ m1.m22 = m22;
+ }
+
+ /**
+ * Replaces the upper 3x3 matrix values of this matrix with the values in the
+ * matrix m1.
+ *
+ * @param m1
+ * The matrix that will be the new upper 3x3
+ */
+ public void setRotationScale(M3 m1) {
+ m00 = m1.m00;
+ m01 = m1.m01;
+ m02 = m1.m02;
+ m10 = m1.m10;
+ m11 = m1.m11;
+ m12 = m1.m12;
+ m20 = m1.m20;
+ m21 = m1.m21;
+ m22 = m1.m22;
+ }
+
+ /**
+ * Sets the specified row of this matrix4f to the four values provided.
+ *
+ * @param row
+ * the row number to be modified (zero indexed)
+ * @param v
+ * the replacement row
+ */
+ public void setRowA(int row, float v[]) {
+ if (row < 3)
+ setRow33(row, v);
+ switch (row) {
+ case 0:
+ m03 = v[3];
+ return;
+ case 1:
+ m13 = v[3];
+ return;
+ case 2:
+ m23 = v[3];
+ return;
+ case 3:
+ m30 = v[0];
+ m31 = v[1];
+ m32 = v[2];
+ m33 = v[3];
+ return;
+ }
+ err();
+ }
+
+ /**
+ * Copies the matrix values in the specified row into the array parameter.
+ *
+ * @param row
+ * the matrix row
+ * @param v
+ * The array into which the matrix row values will be copied
+ */
+ @Override
+ public void getRow(int row, float v[]) {
+ if (row < 3)
+ getRow33(row, v);
+ switch (row) {
+ case 0:
+ v[3] = m03;
+ return;
+ case 1:
+ v[3] = m13;
+ return;
+ case 2:
+ v[3] = m23;
+ return;
+ case 3:
+ v[0] = m30;
+ v[1] = m31;
+ v[2] = m32;
+ v[3] = m33;
+ return;
+ }
+ err();
+ }
+
+ /**
+ * Sets the specified column of this matrix4f to the four values provided.
+ *
+ * @param column
+ * the column number to be modified (zero indexed)
+ * @param x
+ * the first row element
+ * @param y
+ * the second row element
+ * @param z
+ * the third row element
+ * @param w
+ * the fourth row element
+ */
+ public void setColumn4(int column, float x, float y, float z, float w) {
+ if (column == 0) {
+ m00 = x;
+ m10 = y;
+ m20 = z;
+ m30 = w;
+ } else if (column == 1) {
+ m01 = x;
+ m11 = y;
+ m21 = z;
+ m31 = w;
+ } else if (column == 2) {
+ m02 = x;
+ m12 = y;
+ m22 = z;
+ m32 = w;
+ } else if (column == 3) {
+ m03 = x;
+ m13 = y;
+ m23 = z;
+ m33 = w;
+ } else {
+ err();
+ }
+ }
+
+ /**
+ * Sets the specified column of this matrix4f to the four values provided.
+ *
+ * @param column
+ * the column number to be modified (zero indexed)
+ * @param v
+ * the replacement column
+ */
+ public void setColumnA(int column, float v[]) {
+ if (column < 3)
+ setColumn33(column, v);
+ switch (column) {
+ case 0:
+ m30 = v[3];
+ return;
+ case 1:
+ m31 = v[3];
+ return;
+ case 2:
+ m32 = v[3];
+ return;
+ case 3:
+ m03 = v[0];
+ m13 = v[1];
+ m23 = v[2];
+ m33 = v[3];
+ return;
+ default:
+ err();
+ }
+ }
+
+ /**
+ * Copies the matrix values in the specified column into the array parameter.
+ *
+ * @param column
+ * the matrix column
+ * @param v
+ * The array into which the matrix column values will be copied
+ */
+ public void getColumn(int column, float v[]) {
+ if (column < 3)
+ getColumn33(column, v);
+ switch (column) {
+ case 0:
+ v[3] = m30;
+ return;
+ case 1:
+ v[3] = m31;
+ return;
+ case 2:
+ v[3] = m32;
+ return;
+ case 3:
+ v[0] = m03;
+ v[1] = m13;
+ v[2] = m23;
+ v[3] = m33;
+ return;
+ default:
+ err();
+ }
+ }
+
+ /**
+ * Sets the value of this matrix to the matrix difference of itself and matrix
+ * m1 (this = this - m1).
+ *
+ * @param m1
+ * the other matrix
+ */
+ public void sub(M4 m1) {
+ sub33(m1);
+ m03 -= m1.m03;
+ m13 -= m1.m13;
+ m23 -= m1.m23;
+ m30 -= m1.m30;
+ m31 -= m1.m31;
+ m32 -= m1.m32;
+ m33 -= m1.m33;
+ }
+
+ /**
+ * Sets the value of this matrix to its transpose.
+ */
+ public void transpose() {
+ transpose33();
+ float tmp = m03;
+ m03 = m30;
+ m30 = tmp;
+
+ tmp = m13;
+ m13 = m31;
+ m31 = tmp;
+
+ tmp = m23;
+ m23 = m32;
+ m32 = tmp;
+ }
+
+ /**
+ * Sets the value of this matrix to its inverse.
+ * @return this
+ */
+ public M4 invert() {
+ float s = determinant4();
+ if (s == 0.0)
+ return this;
+ s = 1 / s;
+ // alias-safe way.
+ // less *,+,- calculation than expanded expression.
+ set(m11 * (m22 * m33 - m23 * m32) + m12 * (m23 * m31 - m21 * m33) + m13
+ * (m21 * m32 - m22 * m31), m21 * (m02 * m33 - m03 * m32) + m22
+ * (m03 * m31 - m01 * m33) + m23 * (m01 * m32 - m02 * m31), m31
+ * (m02 * m13 - m03 * m12) + m32 * (m03 * m11 - m01 * m13) + m33
+ * (m01 * m12 - m02 * m11), m01 * (m13 * m22 - m12 * m23) + m02
+ * (m11 * m23 - m13 * m21) + m03 * (m12 * m21 - m11 * m22),
+
+ m12 * (m20 * m33 - m23 * m30) + m13 * (m22 * m30 - m20 * m32) + m10
+ * (m23 * m32 - m22 * m33), m22 * (m00 * m33 - m03 * m30) + m23
+ * (m02 * m30 - m00 * m32) + m20 * (m03 * m32 - m02 * m33), m32
+ * (m00 * m13 - m03 * m10) + m33 * (m02 * m10 - m00 * m12) + m30
+ * (m03 * m12 - m02 * m13), m02 * (m13 * m20 - m10 * m23) + m03
+ * (m10 * m22 - m12 * m20) + m00 * (m12 * m23 - m13 * m22),
+
+ m13 * (m20 * m31 - m21 * m30) + m10 * (m21 * m33 - m23 * m31) + m11
+ * (m23 * m30 - m20 * m33), m23 * (m00 * m31 - m01 * m30) + m20
+ * (m01 * m33 - m03 * m31) + m21 * (m03 * m30 - m00 * m33), m33
+ * (m00 * m11 - m01 * m10) + m30 * (m01 * m13 - m03 * m11) + m31
+ * (m03 * m10 - m00 * m13), m03 * (m11 * m20 - m10 * m21) + m00
+ * (m13 * m21 - m11 * m23) + m01 * (m10 * m23 - m13 * m20),
+
+ m10 * (m22 * m31 - m21 * m32) + m11 * (m20 * m32 - m22 * m30) + m12
+ * (m21 * m30 - m20 * m31), m20 * (m02 * m31 - m01 * m32) + m21
+ * (m00 * m32 - m02 * m30) + m22 * (m01 * m30 - m00 * m31), m30
+ * (m02 * m11 - m01 * m12) + m31 * (m00 * m12 - m02 * m10) + m32
+ * (m01 * m10 - m00 * m11), m00 * (m11 * m22 - m12 * m21) + m01
+ * (m12 * m20 - m10 * m22) + m02 * (m10 * m21 - m11 * m20));
+ scale(s);
+ return this;
+ }
+
+ /**
+ * Sets 16 values
+ *
+ * @param m00
+ * @param m01
+ * @param m02
+ * @param m03
+ * @param m10
+ * @param m11
+ * @param m12
+ * @param m13
+ * @param m20
+ * @param m21
+ * @param m22
+ * @param m23
+ * @param m30
+ * @param m31
+ * @param m32
+ * @param m33
+ */
+ private void set(float m00, float m01, float m02, float m03, float m10,
+ float m11, float m12, float m13, float m20, float m21,
+ float m22, float m23, float m30, float m31, float m32,
+ float m33) {
+ this.m00 = m00;
+ this.m01 = m01;
+ this.m02 = m02;
+ this.m03 = m03;
+ this.m10 = m10;
+ this.m11 = m11;
+ this.m12 = m12;
+ this.m13 = m13;
+ this.m20 = m20;
+ this.m21 = m21;
+ this.m22 = m22;
+ this.m23 = m23;
+ this.m30 = m30;
+ this.m31 = m31;
+ this.m32 = m32;
+ this.m33 = m33;
+ }
+ /**
+ * Computes the determinant of this matrix.
+ *
+ * @return the determinant of the matrix
+ */
+ public float determinant4() {
+ // less *,+,- calculation than expanded expression.
+ return (m00 * m11 - m01 * m10) * (m22 * m33 - m23 * m32)
+ - (m00 * m12 - m02 * m10) * (m21 * m33 - m23 * m31)
+ + (m00 * m13 - m03 * m10) * (m21 * m32 - m22 * m31)
+ + (m01 * m12 - m02 * m11) * (m20 * m33 - m23 * m30)
+ - (m01 * m13 - m03 * m11) * (m20 * m32 - m22 * m30)
+ + (m02 * m13 - m03 * m12) * (m20 * m31 - m21 * m30);
+
+ }
+
+ /**
+ * Multiplies each element of this matrix by a scalar.
+ *
+ * @param scalar
+ * The scalar multiplier.
+ */
+ public void scale(float scalar) {
+ mul33(scalar);
+ m03 *= scalar;
+ m13 *= scalar;
+ m23 *= scalar;
+ m30 *= scalar;
+ m31 *= scalar;
+ m32 *= scalar;
+ m33 *= scalar;
+ }
+
+ /**
+ * Sets the value of this matrix to the result of multiplying itself with
+ * matrix m1.
+ *
+ * @param m1
+ * the other matrix
+ */
+ public void mul(M4 m1) {
+ mul2(this, m1);
+ }
+
+ /**
+ * Sets the value of this matrix to the result of multiplying the two argument
+ * matrices together.
+ *
+ * @param m1
+ * the first matrix
+ * @param m2
+ * the second matrix
+ */
+ public void mul2(M4 m1, M4 m2) {
+ // alias-safe way.
+ set(m1.m00 * m2.m00 + m1.m01 * m2.m10 + m1.m02 * m2.m20 + m1.m03 * m2.m30,
+ m1.m00 * m2.m01 + m1.m01 * m2.m11 + m1.m02 * m2.m21 + m1.m03 * m2.m31,
+ m1.m00 * m2.m02 + m1.m01 * m2.m12 + m1.m02 * m2.m22 + m1.m03 * m2.m32,
+ m1.m00 * m2.m03 + m1.m01 * m2.m13 + m1.m02 * m2.m23 + m1.m03 * m2.m33,
+
+ m1.m10 * m2.m00 + m1.m11 * m2.m10 + m1.m12 * m2.m20 + m1.m13 * m2.m30,
+ m1.m10 * m2.m01 + m1.m11 * m2.m11 + m1.m12 * m2.m21 + m1.m13 * m2.m31,
+ m1.m10 * m2.m02 + m1.m11 * m2.m12 + m1.m12 * m2.m22 + m1.m13 * m2.m32,
+ m1.m10 * m2.m03 + m1.m11 * m2.m13 + m1.m12 * m2.m23 + m1.m13 * m2.m33,
+
+ m1.m20 * m2.m00 + m1.m21 * m2.m10 + m1.m22 * m2.m20 + m1.m23 * m2.m30,
+ m1.m20 * m2.m01 + m1.m21 * m2.m11 + m1.m22 * m2.m21 + m1.m23 * m2.m31,
+ m1.m20 * m2.m02 + m1.m21 * m2.m12 + m1.m22 * m2.m22 + m1.m23 * m2.m32,
+ m1.m20 * m2.m03 + m1.m21 * m2.m13 + m1.m22 * m2.m23 + m1.m23 * m2.m33,
+
+ m1.m30 * m2.m00 + m1.m31 * m2.m10 + m1.m32 * m2.m20 + m1.m33 * m2.m30,
+ m1.m30 * m2.m01 + m1.m31 * m2.m11 + m1.m32 * m2.m21 + m1.m33 * m2.m31,
+ m1.m30 * m2.m02 + m1.m31 * m2.m12 + m1.m32 * m2.m22 + m1.m33 * m2.m32,
+ m1.m30 * m2.m03 + m1.m31 * m2.m13 + m1.m32 * m2.m23 + m1.m33 * m2.m33);
+ }
+
+ /**
+ * Transform the vector vec using this Matrix4f and place the result back into
+ * vec.
+ *
+ * @param vec
+ * the single precision vector to be transformed
+ */
+ public void transform(T4 vec) {
+ transform2(vec, vec);
+ }
+
+ /**
+ * Transform the vector vec using this Matrix4f and place the result into
+ * vecOut.
+ *
+ * @param vec
+ * the single precision vector to be transformed
+ * @param vecOut
+ * the vector into which the transformed values are placed
+ */
+ public void transform2(T4 vec, T4 vecOut) {
+ // alias-safe
+ vecOut.set4(m00 * vec.x + m01 * vec.y + m02 * vec.z + m03 * vec.w, m10
+ * vec.x + m11 * vec.y + m12 * vec.z + m13 * vec.w, m20 * vec.x + m21
+ * vec.y + m22 * vec.z + m23 * vec.w, m30 * vec.x + m31 * vec.y + m32
+ * vec.z + m33 * vec.w);
+ }
+
+ /**
+ * Transforms the point parameter with this Matrix4f and places the result
+ * back into point. The fourth element of the point input parameter is assumed
+ * to be one.
+ *
+ * @param point
+ * the input point to be transformed.
+ */
+ public void rotTrans(T3 point) {
+ rotTrans2(point, point);
+ }
+
+ /**
+ * Transforms the point parameter with this Matrix4f and places the result
+ * into pointOut. The fourth element of the point input parameter is assumed to
+ * be one. point may be pointOut
+ *
+ * @param point
+ * the input point to be transformed.
+ * @param pointOut
+ * the transformed point
+ * @return pointOut
+ */
+ public T3 rotTrans2(T3 point, T3 pointOut) {
+ pointOut.set(
+ m00 * point.x + m01 * point.y + m02 * point.z + m03,
+ m10 * point.x + m11 * point.y + m12 * point.z + m13,
+ m20 * point.x + m21 * point.y + m22 * point.z + m23);
+ return pointOut;
+ }
+
+ /**
+ * Sets the value of this matrix to a rotation matrix about the w axis by the
+ * passed angle.
+ *
+ * @param angle
+ * the angle to rotate about the W axis in radians
+ * @return this
+ */
+ public M4 setAsXYRotation(float angle) {
+ setIdentity();
+ double c = Math.cos(angle);
+ double s = Math.sin(angle);
+ m22 = (float) c;
+ m23 = (float) -s;
+ m32 = (float) s;
+ m33 = (float) c;
+ return this;
+ }
+
+ /**
+ * Sets the value of this matrix to a rotation matrix about the w axis by the
+ * passed angle.
+ *
+ * @param angle
+ * the angle to rotate about the W axis in radians
+ * @return this
+ */
+ public M4 setAsYZRotation(float angle) {
+ setIdentity();
+ double c = Math.cos(angle);
+ double s = Math.sin(angle);
+ m00 = (float) c;
+ m03 = (float) -s;
+ m30 = (float) s;
+ m33 = (float) c;
+ return this;
+ }
+
+ /**
+ * Sets the value of this matrix to a rotation matrix about the w axis by the
+ * passed angle.
+ *
+ * @param angle
+ * the angle to rotate about the W axis in radians
+ * @return this
+ */
+ public M4 setAsXZRotation(float angle) {
+ setIdentity();
+ double c = Math.cos(angle);
+ double s = Math.sin(angle);
+ m11 = (float) c;
+ m13 = (float) -s;
+ m31 = (float) s;
+ m33 = (float) c;
+ return this;
+ }
+
+ /**
+ * Returns true if the Object o is of type Matrix4f and all of the data
+ * members of t1 are equal to the corresponding data members in this Matrix4f.
+ *
+ * @param o
+ * the object with which the comparison is made.
+ */
+ @Override
+ public boolean equals(Object o) {
+ if (!(o instanceof M4))
+ return false;
+ M4 m = (M4) o;
+ return (this.m00 == m.m00 && this.m01 == m.m01 && this.m02 == m.m02
+ && this.m03 == m.m03 && this.m10 == m.m10 && this.m11 == m.m11
+ && this.m12 == m.m12 && this.m13 == m.m13 && this.m20 == m.m20
+ && this.m21 == m.m21 && this.m22 == m.m22 && this.m23 == m.m23
+ && this.m30 == m.m30 && this.m31 == m.m31 && this.m32 == m.m32 && this.m33 == m.m33);
+ }
+
+ /**
+ * Returns a hash number based on the data values in this object. Two
+ * different Matrix4f objects with identical data values (ie, returns true for
+ * equals(Matrix4f) ) will return the same hash number. Two objects with
+ * different data members may return the same hash value, although this is not
+ * likely.
+ *
+ * @return the integer hash value
+ */
+ @Override
+ public int hashCode() {
+ return T3.floatToIntBits(m00) ^ T3.floatToIntBits(m01)
+ ^ T3.floatToIntBits(m02) ^ T3.floatToIntBits(m03)
+ ^ T3.floatToIntBits(m10) ^ T3.floatToIntBits(m11)
+ ^ T3.floatToIntBits(m12) ^ T3.floatToIntBits(m13)
+ ^ T3.floatToIntBits(m20) ^ T3.floatToIntBits(m21)
+ ^ T3.floatToIntBits(m22) ^ T3.floatToIntBits(m23)
+ ^ T3.floatToIntBits(m30) ^ T3.floatToIntBits(m31)
+ ^ T3.floatToIntBits(m32) ^ T3.floatToIntBits(m33);
+ }
+
+ /**
+ * Returns a string that contains the values of this Matrix4f.
+ *
+ * @return the String representation
+ */
+ @Override
+ public String toString() {
+ return "[\n [" + m00 + "\t" + m01 + "\t" + m02 + "\t" + m03 + "]"
+ + "\n [" + m10 + "\t" + m11 + "\t" + m12 + "\t" + m13 + "]" + "\n ["
+ + m20 + "\t" + m21 + "\t" + m22 + "\t" + m23 + "]" + "\n [" + m30
+ + "\t" + m31 + "\t" + m32 + "\t" + m33 + "] ]";
+ }
+ public M4 round(float f) {
+ m00 = rnd(m00, f);
+ m01 = rnd(m01, f);
+ m02 = rnd(m02, f);
+ m03 = rnd(m03, f);
+ m10 = rnd(m10, f);
+ m11 = rnd(m11, f);
+ m12 = rnd(m12, f);
+ m13 = rnd(m13, f);
+ m20 = rnd(m20, f);
+ m21 = rnd(m21, f);
+ m22 = rnd(m22, f);
+ m23 = rnd(m23, f);
+ m30 = rnd(m30, f);
+ m31 = rnd(m31, f);
+ m32 = rnd(m32, f);
+ m33 = rnd(m33, f);
+ return this;
+ }
+
+ private float rnd(float n, float f) {
+ return (Math.abs(n) < f ? 0 : n);
+ }
+}
--- /dev/null
+package javajs.util;
+
+/**
+ *
+ * streamlined and refined for Jmol by Bob Hanson
+ *
+ * from http://math.nist.gov/javanumerics/jama/
+ *
+ * Jama = Java Matrix class.
+ *
+ * @author The MathWorks, Inc. and the National Institute of Standards and
+ * Technology.
+ * @version 5 August 1998
+ */
+
+public class Matrix implements Cloneable {
+
+ public double[][] a;
+ protected int m, n;
+
+ /**
+ * Construct a matrix quickly without checking arguments.
+ *
+ * @param a
+ * Two-dimensional array of doubles or null
+ * @param m
+ * Number of rows.
+ * @param n
+ * Number of colums.
+ */
+
+ public Matrix(double[][] a, int m, int n) {
+ this.a = (a == null ? new double[m][n] : a);
+ this.m = m;
+ this.n = n;
+ }
+
+ /**
+ * Get row dimension.
+ *
+ * @return m, the number of rows.
+ */
+
+ public int getRowDimension() {
+ return m;
+ }
+
+ /**
+ * Get column dimension.
+ *
+ * @return n, the number of columns.
+ */
+
+ public int getColumnDimension() {
+ return n;
+ }
+
+ /**
+ * Access the internal two-dimensional array.
+ *
+ * @return Pointer to the two-dimensional array of matrix elements.
+ */
+
+ public double[][] getArray() {
+ return a;
+ }
+
+ /**
+ * Copy the internal two-dimensional array.
+ *
+ * @return Two-dimensional array copy of matrix elements.
+ */
+
+ public double[][] getArrayCopy() {
+ double[][] x = new double[m][n];
+ for (int i = m; --i >= 0;)
+ for (int j = n; --j >= 0;)
+ x[i][j] = a[i][j];
+ return x;
+ }
+
+ /**
+ * Make a deep copy of a matrix
+ *
+ * @return copy
+ */
+
+ public Matrix copy() {
+ Matrix x = new Matrix(null, m, n);
+ double[][] c = x.a;
+ for (int i = m; --i >= 0;)
+ for (int j = n; --j >= 0;)
+ c[i][j] = a[i][j];
+ return x;
+ }
+
+ /**
+ * Clone the Matrix object.
+ */
+
+ @Override
+ public Object clone() {
+ return copy();
+ }
+
+ /**
+ * Get a submatrix.
+ *
+ * @param i0
+ * Initial row index
+ * @param j0
+ * Initial column index
+ * @param nrows
+ * Number of rows
+ * @param ncols
+ * Number of columns
+ * @return submatrix
+ *
+ */
+
+ public Matrix getSubmatrix(int i0, int j0, int nrows, int ncols) {
+ Matrix x = new Matrix(null, nrows, ncols);
+ double[][] xa = x.a;
+ for (int i = nrows; --i >= 0;)
+ for (int j = ncols; --j >= 0;)
+ xa[i][j] = a[i0 + i][j0 + j];
+ return x;
+ }
+
+ /**
+ * Get a submatrix for a give number of columns and selected row set.
+ *
+ * @param r
+ * Array of row indices.
+ * @param n
+ * number of rows
+ * @return submatrix
+ */
+
+ public Matrix getMatrixSelected(int[] r, int n) {
+ Matrix x = new Matrix(null, r.length, n);
+ double[][] xa = x.a;
+ for (int i = r.length; --i >= 0;) {
+ double[] b = a[r[i]];
+ for (int j = n; --j >= 0;)
+ xa[i][j] = b[j];
+ }
+ return x;
+ }
+
+ /**
+ * Matrix transpose.
+ *
+ * @return A'
+ */
+
+ public Matrix transpose() {
+ Matrix x = new Matrix(null, n, m);
+ double[][] c = x.a;
+ for (int i = m; --i >= 0;)
+ for (int j = n; --j >= 0;)
+ c[j][i] = a[i][j];
+ return x;
+ }
+
+ /**
+ * add two matrices
+ * @param b
+ * @return new Matrix this + b
+ */
+ public Matrix add(Matrix b) {
+ return scaleAdd(b, 1);
+ }
+
+ /**
+ * subtract two matrices
+ * @param b
+ * @return new Matrix this - b
+ */
+ public Matrix sub(Matrix b) {
+ return scaleAdd(b, -1);
+ }
+
+ /**
+ * X = A + B*scale
+ * @param b
+ * @param scale
+ * @return X
+ *
+ */
+ public Matrix scaleAdd(Matrix b, double scale) {
+ Matrix x = new Matrix(null, m, n);
+ double[][] xa = x.a;
+ double[][] ba = b.a;
+ for (int i = m; --i >= 0;)
+ for (int j = n; --j >= 0;)
+ xa[i][j] = ba[i][j] * scale + a[i][j];
+ return x;
+ }
+
+ /**
+ * Linear algebraic matrix multiplication, A * B
+ *
+ * @param b
+ * another matrix
+ * @return Matrix product, A * B or null for wrong dimension
+ */
+
+ public Matrix mul(Matrix b) {
+ if (b.m != n)
+ return null;
+ Matrix x = new Matrix(null, m, b.n);
+ double[][] xa = x.a;
+ double[][] ba = b.a;
+ for (int j = b.n; --j >= 0;)
+ for (int i = m; --i >= 0;) {
+ double[] arowi = a[i];
+ double s = 0;
+ for (int k = n; --k >= 0;)
+ s += arowi[k] * ba[k][j];
+ xa[i][j] = s;
+ }
+ return x;
+ }
+
+ /**
+ * Matrix inverse or pseudoinverse
+ *
+ * @return inverse (m == n) or pseudoinverse (m != n)
+ */
+
+ public Matrix inverse() {
+ return new LUDecomp(m, n).solve(identity(m, m), n);
+ }
+
+ /**
+ * Matrix trace.
+ *
+ * @return sum of the diagonal elements.
+ */
+
+ public double trace() {
+ double t = 0;
+ for (int i = Math.min(m, n); --i >= 0;)
+ t += a[i][i];
+ return t;
+ }
+
+ /**
+ * Generate identity matrix
+ *
+ * @param m
+ * Number of rows.
+ * @param n
+ * Number of columns.
+ * @return An m-by-n matrix with ones on the diagonal and zeros elsewhere.
+ */
+
+ public static Matrix identity(int m, int n) {
+ Matrix x = new Matrix(null, m, n);
+ double[][] xa = x.a;
+ for (int i = Math.min(m, n); --i >= 0;)
+ xa[i][i] = 1;
+ return x;
+ }
+
+ /**
+ * similarly to M3/M4 standard rotation/translation matrix
+ * we set a rotationTranslation matrix to be:
+ *
+ * [ nxn rot nx1 trans
+ *
+ * 1xn 0 1x1 1 ]
+ *
+ *
+ * @return rotation matrix
+ */
+ public Matrix getRotation() {
+ return getSubmatrix(0, 0, m - 1, n - 1);
+ }
+
+ public Matrix getTranslation() {
+ return getSubmatrix(0, n - 1, m - 1, 1);
+ }
+
+ public static Matrix newT(T3 r, boolean asColumn) {
+ return (asColumn ? new Matrix(new double[][] { new double[] { r.x },
+ new double[] { r.y }, new double[] { r.z } }, 3, 1) : new Matrix(
+ new double[][] { new double[] { r.x, r.y, r.z } }, 1, 3));
+ }
+
+ @Override
+ public String toString() {
+ String s = "[\n";
+ for (int i = 0; i < m; i++) {
+ s += " [";
+ for (int j = 0; j < n; j++)
+ s += " " + a[i][j];
+ s += "]\n";
+ }
+ s += "]";
+ return s;
+ }
+
+ /**
+ *
+ * Edited down by Bob Hanson for minimum needed by Jmol -- just constructor
+ * and solve
+ *
+ * LU Decomposition.
+ * <P>
+ * For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n unit
+ * lower triangular matrix L, an n-by-n upper triangular matrix U, and a
+ * permutation vector piv of length m so that A(piv,:) = L*U. If m < n, then L
+ * is m-by-m and U is m-by-n.
+ * <P>
+ * The LU decompostion with pivoting always exists, even if the matrix is
+ * singular, so the constructor will never fail. The primary use of the LU
+ * decomposition is in the solution of square systems of simultaneous linear
+ * equations. This will fail if isNonsingular() returns false.
+ */
+
+ private class LUDecomp {
+
+ /* ------------------------
+ Class variables
+ * ------------------------ */
+
+ /**
+ * Array for internal storage of decomposition.
+ *
+ */
+ private double[][] LU;
+
+ /**
+ * Internal storage of pivot vector.
+ *
+ */
+ private int[] piv;
+
+ private int pivsign;
+
+ /* ------------------------
+ Constructor
+ * ------------------------ */
+
+ /**
+ * LU Decomposition Structure to access L, U and piv.
+ * @param m
+ * @param n
+ *
+ */
+
+ protected LUDecomp(int m, int n) {
+
+ // Use a "left-looking", dot-product, Crout/Doolittle algorithm.
+
+ LU = getArrayCopy();
+ piv = new int[m];
+ for (int i = m; --i >= 0;)
+ piv[i] = i;
+ pivsign = 1;
+ double[] LUrowi;
+ double[] LUcolj = new double[m];
+
+ // Outer loop.
+
+ for (int j = 0; j < n; j++) {
+
+ // Make a copy of the j-th column to localize references.
+
+ for (int i = m; --i >= 0;)
+ LUcolj[i] = LU[i][j];
+
+ // Apply previous transformations.
+
+ for (int i = m; --i >= 0;) {
+ LUrowi = LU[i];
+
+ // Most of the time is spent in the following dot product.
+
+ int kmax = Math.min(i, j);
+ double s = 0.0;
+ for (int k = kmax; --k >= 0;)
+ s += LUrowi[k] * LUcolj[k];
+
+ LUrowi[j] = LUcolj[i] -= s;
+ }
+
+ // Find pivot and exchange if necessary.
+
+ int p = j;
+ for (int i = m; --i > j;)
+ if (Math.abs(LUcolj[i]) > Math.abs(LUcolj[p]))
+ p = i;
+ if (p != j) {
+ for (int k = n; --k >= 0;) {
+ double t = LU[p][k];
+ LU[p][k] = LU[j][k];
+ LU[j][k] = t;
+ }
+ int k = piv[p];
+ piv[p] = piv[j];
+ piv[j] = k;
+ pivsign = -pivsign;
+ }
+
+ // Compute multipliers.
+
+ if (j < m & LU[j][j] != 0.0)
+ for (int i = m; --i > j;)
+ LU[i][j] /= LU[j][j];
+ }
+ }
+
+ /* ------------------------
+ default Methods
+ * ------------------------ */
+
+ /**
+ * Solve A*X = B
+ *
+ * @param b
+ * A Matrix with as many rows as A and any number of columns.
+ * @param n
+ * @return X so that L*U*X = B(piv,:) or null for wrong size or singular matrix
+ */
+
+ protected Matrix solve(Matrix b, int n) {
+ for (int j = 0; j < n; j++)
+ if (LU[j][j] == 0)
+ return null; // matrix is singular
+
+ // Copy right hand side with pivoting
+ int nx = b.n;
+ Matrix x = b.getMatrixSelected(piv, nx);
+ double[][] a = x.a;
+
+ // Solve L*Y = B(piv,:)
+ for (int k = 0; k < n; k++)
+ for (int i = k + 1; i < n; i++)
+ for (int j = 0; j < nx; j++)
+ a[i][j] -= a[k][j] * LU[i][k];
+
+ // Solve U*X = Y;
+ for (int k = n; --k >= 0;) {
+ for (int j = nx; --j >= 0;)
+ a[k][j] /= LU[k][k];
+ for (int i = k; --i >= 0;)
+ for (int j = nx; --j >= 0;)
+ a[i][j] -= a[k][j] * LU[i][k];
+ }
+ return x;
+ }
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2005-11-10 09:52:44 -0600 (Thu, 10 Nov 2005) $
+ * $Revision: 4255 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.util;
+
+import javajs.api.EigenInterface;
+
+import javajs.api.Interface;
+
+
+
+
+//import org.jmol.script.T;
+
+final public class Measure {
+
+ public final static float radiansPerDegree = (float) (2 * Math.PI / 360);
+
+ public static float computeAngle(T3 pointA, T3 pointB, T3 pointC, V3 vectorBA, V3 vectorBC, boolean asDegrees) {
+ vectorBA.sub2(pointA, pointB);
+ vectorBC.sub2(pointC, pointB);
+ float angle = vectorBA.angle(vectorBC);
+ return (asDegrees ? angle / radiansPerDegree : angle);
+ }
+
+ public static float computeAngleABC(T3 pointA, T3 pointB, T3 pointC, boolean asDegrees) {
+ V3 vectorBA = new V3();
+ V3 vectorBC = new V3();
+ return computeAngle(pointA, pointB, pointC, vectorBA, vectorBC, asDegrees);
+ }
+
+ public static float computeTorsion(T3 p1, T3 p2, T3 p3, T3 p4, boolean asDegrees) {
+
+ float ijx = p1.x - p2.x;
+ float ijy = p1.y - p2.y;
+ float ijz = p1.z - p2.z;
+
+ float kjx = p3.x - p2.x;
+ float kjy = p3.y - p2.y;
+ float kjz = p3.z - p2.z;
+
+ float klx = p3.x - p4.x;
+ float kly = p3.y - p4.y;
+ float klz = p3.z - p4.z;
+
+ float ax = ijy * kjz - ijz * kjy;
+ float ay = ijz * kjx - ijx * kjz;
+ float az = ijx * kjy - ijy * kjx;
+ float cx = kjy * klz - kjz * kly;
+ float cy = kjz * klx - kjx * klz;
+ float cz = kjx * kly - kjy * klx;
+
+ float ai2 = 1f / (ax * ax + ay * ay + az * az);
+ float ci2 = 1f / (cx * cx + cy * cy + cz * cz);
+
+ float ai = (float) Math.sqrt(ai2);
+ float ci = (float) Math.sqrt(ci2);
+ float denom = ai * ci;
+ float cross = ax * cx + ay * cy + az * cz;
+ float cosang = cross * denom;
+ if (cosang > 1) {
+ cosang = 1;
+ }
+ if (cosang < -1) {
+ cosang = -1;
+ }
+
+ float torsion = (float) Math.acos(cosang);
+ float dot = ijx * cx + ijy * cy + ijz * cz;
+ float absDot = Math.abs(dot);
+ torsion = (dot / absDot > 0) ? torsion : -torsion;
+ return (asDegrees ? torsion / radiansPerDegree : torsion);
+ }
+
+ /**
+ * This method calculates measures relating to two points in space
+ * with related quaternion frame difference. It is used in Jmol for
+ * calculating straightness and many other helical quantities.
+ *
+ * @param a
+ * @param b
+ * @param dq
+ * @return new T3[] { pt_a_prime, n, r, P3.new3(theta, pitch, residuesPerTurn), pt_b_prime };
+ */
+ public static T3[] computeHelicalAxis(P3 a, P3 b, Quat dq) {
+
+ // b
+ // | /|
+ // | / |
+ // | / |
+ // |/ c
+ // b'+ / \
+ // | / \ Vcb = Vab . n
+ // n | / \d Vda = (Vcb - Vab) / 2
+ // |/theta \
+ // a'+---------a
+ // r
+
+ V3 vab = new V3();
+ vab.sub2(b, a);
+ /*
+ * testing here to see if directing the normal makes any difference -- oddly
+ * enough, it does not. When n = -n and theta = -theta vab.n is reversed,
+ * and that magnitude is multiplied by n in generating the A'-B' vector.
+ *
+ * a negative angle implies a left-handed axis (sheets)
+ */
+ float theta = dq.getTheta();
+ V3 n = dq.getNormal();
+ float v_dot_n = vab.dot(n);
+ if (Math.abs(v_dot_n) < 0.0001f)
+ v_dot_n = 0;
+ V3 va_prime_d = new V3();
+ va_prime_d.cross(vab, n);
+ if (va_prime_d.dot(va_prime_d) != 0)
+ va_prime_d.normalize();
+ V3 vda = new V3();
+ V3 vcb = V3.newV(n);
+ if (v_dot_n == 0)
+ v_dot_n = PT.FLOAT_MIN_SAFE; // allow for perpendicular axis to vab
+ vcb.scale(v_dot_n);
+ vda.sub2(vcb, vab);
+ vda.scale(0.5f);
+ va_prime_d.scale(theta == 0 ? 0 : (float) (vda.length() / Math.tan(theta
+ / 2 / 180 * Math.PI)));
+ V3 r = V3.newV(va_prime_d);
+ if (theta != 0)
+ r.add(vda);
+ P3 pt_a_prime = P3.newP(a);
+ pt_a_prime.sub(r);
+ // already done this. ??
+ if (v_dot_n != PT.FLOAT_MIN_SAFE)
+ n.scale(v_dot_n);
+ // must calculate directed angle:
+ P3 pt_b_prime = P3.newP(pt_a_prime);
+ pt_b_prime.add(n);
+ theta = computeTorsion(a, pt_a_prime, pt_b_prime, b, true);
+ if (Float.isNaN(theta) || r.length() < 0.0001f)
+ theta = dq.getThetaDirectedV(n); // allow for r = 0
+ // anything else is an array
+ float residuesPerTurn = Math.abs(theta == 0 ? 0 : 360f / theta);
+ float pitch = Math.abs(v_dot_n == PT.FLOAT_MIN_SAFE ? 0 : n.length()
+ * (theta == 0 ? 1 : 360f / theta));
+ return new T3[] { pt_a_prime, n, r, P3.new3(theta, pitch, residuesPerTurn), pt_b_prime };
+ }
+
+ public static P4 getPlaneThroughPoints(T3 pointA,
+ T3 pointB,
+ T3 pointC, V3 vNorm,
+ V3 vAB, P4 plane) {
+ float w = getNormalThroughPoints(pointA, pointB, pointC, vNorm, vAB);
+ plane.set4(vNorm.x, vNorm.y, vNorm.z, w);
+ return plane;
+ }
+
+ public static void getPlaneThroughPoint(T3 pt, V3 normal, P4 plane) {
+ plane.set4(normal.x, normal.y, normal.z, -normal.dot(pt));
+ }
+
+ public static float distanceToPlane(P4 plane, T3 pt) {
+ return (plane == null ? Float.NaN
+ : (plane.dot(pt) + plane.w) / (float) Math.sqrt(plane.dot(plane)));
+ }
+
+ public static float directedDistanceToPlane(P3 pt, P4 plane, P3 ptref) {
+ float f = plane.dot(pt) + plane.w;
+ float f1 = plane.dot(ptref) + plane.w;
+ return Math.signum(f1) * f / (float) Math.sqrt(plane.dot(plane));
+ }
+
+ public static float distanceToPlaneD(P4 plane, float d, P3 pt) {
+ return (plane == null ? Float.NaN : (plane.dot(pt) + plane.w) / d);
+ }
+
+ public static float distanceToPlaneV(V3 norm, float w, P3 pt) {
+ return (norm == null ? Float.NaN
+ : (norm.dot(pt) + w) / (float) Math.sqrt(norm.dot(norm)));
+ }
+
+ /**
+ * note that if vAB or vAC is dispensible, vNormNorm can be one of them
+ * @param pointA
+ * @param pointB
+ * @param pointC
+ * @param vNormNorm
+ * @param vAB
+ */
+ public static void calcNormalizedNormal(T3 pointA, T3 pointB,
+ T3 pointC, T3 vNormNorm, T3 vAB) {
+ vAB.sub2(pointB, pointA);
+ vNormNorm.sub2(pointC, pointA);
+ vNormNorm.cross(vAB, vNormNorm);
+ vNormNorm.normalize();
+ }
+
+ public static float getDirectedNormalThroughPoints(T3 pointA,
+ T3 pointB, T3 pointC, T3 ptRef, V3 vNorm,
+ V3 vAB) {
+ // for x = plane({atomno=1}, {atomno=2}, {atomno=3}, {atomno=4})
+ float nd = getNormalThroughPoints(pointA, pointB, pointC, vNorm, vAB);
+ if (ptRef != null) {
+ P3 pt0 = P3.newP(pointA);
+ pt0.add(vNorm);
+ float d = pt0.distance(ptRef);
+ pt0.sub2(pointA, vNorm);
+ if (d > pt0.distance(ptRef)) {
+ vNorm.scale(-1);
+ nd = -nd;
+ }
+ }
+ return nd;
+ }
+
+ /**
+ * if vAC is dispensible vNorm can be vAC
+ * @param pointA
+ * @param pointB
+ * @param pointC
+ * @param vNorm
+ * @param vTemp
+ * @return w
+ */
+ public static float getNormalThroughPoints(T3 pointA, T3 pointB,
+ T3 pointC, T3 vNorm, T3 vTemp) {
+ // for Polyhedra
+ calcNormalizedNormal(pointA, pointB, pointC, vNorm, vTemp);
+ // ax + by + cz + d = 0
+ // so if a point is in the plane, then N dot X = -d
+ vTemp.setT(pointA);
+ return -vTemp.dot(vNorm);
+ }
+
+ public static void getPlaneProjection(P3 pt, P4 plane, P3 ptProj, V3 vNorm) {
+ float dist = distanceToPlane(plane, pt);
+ vNorm.set(plane.x, plane.y, plane.z);
+ vNorm.normalize();
+ vNorm.scale(-dist);
+ ptProj.add2(pt, vNorm);
+ }
+
+ /**
+ *
+ * @param ptCenter
+ * @param ptA
+ * @param ptB
+ * @param ptC
+ * @param isOutward
+ * @param normal set to be opposite to direction of ptCenter from ABC
+ * @param vTemp
+ * @return true if winding is CCW; false if CW
+ */
+ public static boolean getNormalFromCenter(P3 ptCenter, P3 ptA, P3 ptB, P3 ptC,
+ boolean isOutward, V3 normal, V3 vTemp) {
+ float d = getNormalThroughPoints(ptA, ptB, ptC, normal, vTemp);
+ boolean isReversed = (distanceToPlaneV(normal, d, ptCenter) > 0);
+ if (isReversed == isOutward)
+ normal.scale(-1f);
+ return !isReversed;
+ }
+
+ public final static V3 axisY = V3.new3(0, 1, 0);
+
+ public static void getNormalToLine(P3 pointA, P3 pointB,
+ V3 vNormNorm) {
+ // vector in xy plane perpendicular to a line between two points RMH
+ vNormNorm.sub2(pointA, pointB);
+ vNormNorm.cross(vNormNorm, axisY);
+ vNormNorm.normalize();
+ if (Float.isNaN(vNormNorm.x))
+ vNormNorm.set(1, 0, 0);
+ }
+
+ public static void getBisectingPlane(P3 pointA, V3 vAB,
+ T3 ptTemp, V3 vTemp, P4 plane) {
+ ptTemp.scaleAdd2(0.5f, vAB, pointA);
+ vTemp.setT(vAB);
+ vTemp.normalize();
+ getPlaneThroughPoint(ptTemp, vTemp, plane);
+ }
+
+ public static void projectOntoAxis(P3 point, P3 axisA,
+ V3 axisUnitVector,
+ V3 vectorProjection) {
+ vectorProjection.sub2(point, axisA);
+ float projectedLength = vectorProjection.dot(axisUnitVector);
+ point.scaleAdd2(projectedLength, axisUnitVector, axisA);
+ vectorProjection.sub2(point, axisA);
+ }
+
+ public static void calcBestAxisThroughPoints(P3[] points, P3 axisA,
+ V3 axisUnitVector,
+ V3 vectorProjection,
+ int nTriesMax) {
+ // just a crude starting point.
+
+ int nPoints = points.length;
+ axisA.setT(points[0]);
+ axisUnitVector.sub2(points[nPoints - 1], axisA);
+ axisUnitVector.normalize();
+
+ /*
+ * We now calculate the least-squares 3D axis
+ * through the helix alpha carbons starting with Vo
+ * as a first approximation.
+ *
+ * This uses the simple 0-centered least squares fit:
+ *
+ * Y = M cross Xi
+ *
+ * minimizing R^2 = SUM(|Y - Yi|^2)
+ *
+ * where Yi is the vector PERPENDICULAR of the point onto axis Vo
+ * and Xi is the vector PROJECTION of the point onto axis Vo
+ * and M is a vector adjustment
+ *
+ * M = SUM_(Xi cross Yi) / sum(|Xi|^2)
+ *
+ * from which we arrive at:
+ *
+ * V = Vo + (M cross Vo)
+ *
+ * Basically, this is just a 3D version of a
+ * standard 2D least squares fit to a line, where we would say:
+ *
+ * y = m xi + b
+ *
+ * D = n (sum xi^2) - (sum xi)^2
+ *
+ * m = [(n sum xiyi) - (sum xi)(sum yi)] / D
+ * b = [(sum yi) (sum xi^2) - (sum xi)(sum xiyi)] / D
+ *
+ * but here we demand that the line go through the center, so we
+ * require (sum xi) = (sum yi) = 0, so b = 0 and
+ *
+ * m = (sum xiyi) / (sum xi^2)
+ *
+ * In 3D we do the same but
+ * instead of x we have Vo,
+ * instead of multiplication we use cross products
+ *
+ * A bit of iteration is necessary.
+ *
+ * Bob Hanson 11/2006
+ *
+ */
+
+ calcAveragePointN(points, nPoints, axisA);
+
+ int nTries = 0;
+ while (nTries++ < nTriesMax
+ && findAxis(points, nPoints, axisA, axisUnitVector, vectorProjection) > 0.001) {
+ }
+
+ /*
+ * Iteration here gets the job done.
+ * We now find the projections of the endpoints onto the axis
+ *
+ */
+
+ P3 tempA = P3.newP(points[0]);
+ projectOntoAxis(tempA, axisA, axisUnitVector, vectorProjection);
+ axisA.setT(tempA);
+ }
+
+ public static float findAxis(P3[] points, int nPoints, P3 axisA,
+ V3 axisUnitVector, V3 vectorProjection) {
+ V3 sumXiYi = new V3();
+ V3 vTemp = new V3();
+ P3 pt = new P3();
+ P3 ptProj = new P3();
+ V3 a = V3.newV(axisUnitVector);
+
+ float sum_Xi2 = 0;
+ for (int i = nPoints; --i >= 0;) {
+ pt.setT(points[i]);
+ ptProj.setT(pt);
+ projectOntoAxis(ptProj, axisA, axisUnitVector,
+ vectorProjection);
+ vTemp.sub2(pt, ptProj);
+ //sum_Yi2 += vTemp.lengthSquared();
+ vTemp.cross(vectorProjection, vTemp);
+ sumXiYi.add(vTemp);
+ sum_Xi2 += vectorProjection.lengthSquared();
+ }
+ V3 m = V3.newV(sumXiYi);
+ m.scale(1 / sum_Xi2);
+ vTemp.cross(m, axisUnitVector);
+ axisUnitVector.add(vTemp);
+ axisUnitVector.normalize();
+ //check for change in direction by measuring vector difference length
+ vTemp.sub2(axisUnitVector, a);
+ return vTemp.length();
+ }
+
+
+ public static void calcAveragePoint(P3 pointA, P3 pointB,
+ P3 pointC) {
+ pointC.set((pointA.x + pointB.x) / 2, (pointA.y + pointB.y) / 2,
+ (pointA.z + pointB.z) / 2);
+ }
+
+ public static void calcAveragePointN(P3[] points, int nPoints,
+ P3 averagePoint) {
+ averagePoint.setT(points[0]);
+ for (int i = 1; i < nPoints; i++)
+ averagePoint.add(points[i]);
+ averagePoint.scale(1f / nPoints);
+ }
+
+ public static Lst<P3> transformPoints(Lst<P3> vPts, M4 m4, P3 center) {
+ Lst<P3> v = new Lst<P3>();
+ for (int i = 0; i < vPts.size(); i++) {
+ P3 pt = P3.newP(vPts.get(i));
+ pt.sub(center);
+ m4.rotTrans(pt);
+ pt.add(center);
+ v.addLast(pt);
+ }
+ return v;
+ }
+
+ public static boolean isInTetrahedron(P3 pt, P3 ptA, P3 ptB,
+ P3 ptC, P3 ptD,
+ P4 plane, V3 vTemp,
+ V3 vTemp2, boolean fullyEnclosed) {
+ boolean b = (distanceToPlane(getPlaneThroughPoints(ptC, ptD, ptA, vTemp, vTemp2, plane), pt) >= 0);
+ if (b != (distanceToPlane(getPlaneThroughPoints(ptA, ptD, ptB, vTemp, vTemp2, plane), pt) >= 0))
+ return false;
+ if (b != (distanceToPlane(getPlaneThroughPoints(ptB, ptD, ptC, vTemp, vTemp2, plane), pt) >= 0))
+ return false;
+ float d = distanceToPlane(getPlaneThroughPoints(ptA, ptB, ptC, vTemp, vTemp2, plane), pt);
+ if (fullyEnclosed)
+ return (b == (d >= 0));
+ float d1 = distanceToPlane(plane, ptD);
+ return d1 * d <= 0 || Math.abs(d1) > Math.abs(d);
+ }
+
+
+ /**
+ *
+ * @param plane1
+ * @param plane2
+ * @return [ point, vector ] or []
+ */
+ public static Lst<Object> getIntersectionPP(P4 plane1, P4 plane2) {
+ float a1 = plane1.x;
+ float b1 = plane1.y;
+ float c1 = plane1.z;
+ float d1 = plane1.w;
+ float a2 = plane2.x;
+ float b2 = plane2.y;
+ float c2 = plane2.z;
+ float d2 = plane2.w;
+ V3 norm1 = V3.new3(a1, b1, c1);
+ V3 norm2 = V3.new3(a2, b2, c2);
+ V3 nxn = new V3();
+ nxn.cross(norm1, norm2);
+ float ax = Math.abs(nxn.x);
+ float ay = Math.abs(nxn.y);
+ float az = Math.abs(nxn.z);
+ float x, y, z, diff;
+ int type = (ax > ay ? (ax > az ? 1 : 3) : ay > az ? 2 : 3);
+ switch(type) {
+ case 1:
+ x = 0;
+ diff = (b1 * c2 - b2 * c1);
+ if (Math.abs(diff) < 0.01) return null;
+ y = (c1 * d2 - c2 * d1) / diff;
+ z = (b2 * d1 - d2 * b1) / diff;
+ break;
+ case 2:
+ diff = (a1 * c2 - a2 * c1);
+ if (Math.abs(diff) < 0.01) return null;
+ x = (c1 * d2 - c2 * d1) / diff;
+ y = 0;
+ z = (a2 * d1 - d2 * a1) / diff;
+ break;
+ case 3:
+ default:
+ diff = (a1 * b2 - a2 * b1);
+ if (Math.abs(diff) < 0.01) return null;
+ x = (b1 * d2 - b2 * d1) / diff;
+ y = (a2 * d1 - d2 * a1) / diff;
+ z = 0;
+ }
+ Lst<Object>list = new Lst<Object>();
+ list.addLast(P3.new3(x, y, z));
+ nxn.normalize();
+ list.addLast(nxn);
+ return list;
+ }
+
+ /**
+ *
+ * @param pt1 point on line
+ * @param v unit vector of line
+ * @param plane
+ * @param ptRet point of intersection of line with plane
+ * @param tempNorm
+ * @param vTemp
+ * @return ptRtet
+ */
+ public static P3 getIntersection(P3 pt1, V3 v,
+ P4 plane, P3 ptRet, V3 tempNorm, V3 vTemp) {
+ getPlaneProjection(pt1, plane, ptRet, tempNorm);
+ tempNorm.set(plane.x, plane.y, plane.z);
+ tempNorm.normalize();
+ if (v == null)
+ v = V3.newV(tempNorm);
+ float l_dot_n = v.dot(tempNorm);
+ if (Math.abs(l_dot_n) < 0.01) return null;
+ vTemp.sub2(ptRet, pt1);
+ ptRet.scaleAdd2(vTemp.dot(tempNorm) / l_dot_n, v, pt1);
+ return ptRet;
+ }
+
+ /*
+ * public static Point3f getTriangleIntersection(Point3f a1, Point3f a2,
+ * Point3f a3, Point4f plane, Point3f b1, Point3f b2, Point3f b3, Vector3f
+ * vNorm, Vector3f vTemp, Point3f ptRet, Point3f ptTemp, Vector3f vTemp2,
+ * Point4f pTemp, Vector3f vTemp3) {
+ *
+ * if (getTriangleIntersection(b1, b2, a1, a2, a3, vTemp, plane, vNorm,
+ * vTemp2, vTemp3, ptRet, ptTemp)) return ptRet; if
+ * (getTriangleIntersection(b2, b3, a1, a2, a3, vTemp, plane, vNorm, vTemp2,
+ * vTemp3, ptRet, ptTemp)) return ptRet; if (getTriangleIntersection(b3, b1,
+ * a1, a2, a3, vTemp, plane, vNorm, vTemp2, vTemp3, ptRet, ptTemp)) return
+ * ptRet; return null; }
+ */
+ /*
+ * public static boolean getTriangleIntersection(Point3f b1, Point3f b2,
+ * Point3f a1, Point3f a2, Point3f a3, Vector3f vTemp, Point4f plane, Vector3f
+ * vNorm, Vector3f vTemp2, Vector3f vTemp3, Point3f ptRet, Point3f ptTemp) {
+ * if (distanceToPlane(plane, b1) * distanceToPlane(plane, b2) >= 0) return
+ * false; vTemp.sub(b2, b1); vTemp.normalize(); if (getIntersection(b1, vTemp,
+ * plane, ptRet, vNorm, vTemp2) != null) { if (isInTriangle(ptRet, a1, a2, a3,
+ * vTemp, vTemp2, vTemp3)) return true; } return false; } private static
+ * boolean isInTriangle(Point3f p, Point3f a, Point3f b, Point3f c, Vector3f
+ * v0, Vector3f v1, Vector3f v2) { // from
+ * http://www.blackpawn.com/texts/pointinpoly/default.html // Compute
+ * barycentric coordinates v0.sub(c, a); v1.sub(b, a); v2.sub(p, a); float
+ * dot00 = v0.dot(v0); float dot01 = v0.dot(v1); float dot02 = v0.dot(v2);
+ * float dot11 = v1.dot(v1); float dot12 = v1.dot(v2); float invDenom = 1 /
+ * (dot00 * dot11 - dot01 * dot01); float u = (dot11 * dot02 - dot01 * dot12)
+ * * invDenom; float v = (dot00 * dot12 - dot01 * dot02) * invDenom; return (u
+ * > 0 && v > 0 && u + v < 1); }
+ */
+
+ /**
+ * Closed-form solution of absolute orientation requiring 1:1 mapping of
+ * positions.
+ *
+ * @param centerAndPoints
+ * @param retStddev
+ * @return unit quaternion representation rotation
+ *
+ * @author hansonr Bob Hanson
+ *
+ */
+ public static Quat calculateQuaternionRotation(P3[][] centerAndPoints,
+ float[] retStddev) {
+ /*
+ * see Berthold K. P. Horn,
+ * "Closed-form solution of absolute orientation using unit quaternions" J.
+ * Opt. Soc. Amer. A, 1987, Vol. 4, pp. 629-642
+ * http://www.opticsinfobase.org/viewmedia.cfm?uri=josaa-4-4-629&seq=0
+ *
+ *
+ * A similar treatment was developed independently (and later!) by G.
+ * Kramer, in G. R. Kramer,
+ * "Superposition of Molecular Structures Using Quaternions" Molecular
+ * Simulation, 1991, Vol. 7, pp. 113-119.
+ *
+ * In that treatment there is a lot of unnecessary calculation along the
+ * trace of matrix M (eqn 20). I'm not sure why the extra x^2 + y^2 + z^2 +
+ * x'^2 + y'^2 + z'^2 is in there, but they are unnecessary and only
+ * contribute to larger numerical averaging errors and additional processing
+ * time, as far as I can tell. Adding aI, where a is a scalar and I is the
+ * 4x4 identity just offsets the eigenvalues but doesn't change the
+ * eigenvectors.
+ *
+ * and Lydia E. Kavraki, "Molecular Distance Measures"
+ * http://cnx.org/content/m11608/latest/
+ */
+
+
+ retStddev[1] = Float.NaN;
+ Quat q = new Quat();
+ P3[] ptsA = centerAndPoints[0];
+ P3[] ptsB = centerAndPoints[1];
+ int nPts = ptsA.length - 1;
+ if (nPts < 2 || ptsA.length != ptsB.length)
+ return q;
+ double Sxx = 0, Sxy = 0, Sxz = 0, Syx = 0, Syy = 0, Syz = 0, Szx = 0, Szy = 0, Szz = 0;
+ P3 ptA = new P3();
+ P3 ptB = new P3();
+ P3 ptA0 = ptsA[0];
+ P3 ptB0 = ptsB[0];
+ for (int i = nPts + 1; --i >= 1;) {
+ ptA.sub2(ptsA[i], ptA0);
+ ptB.sub2(ptsB[i], ptB0);
+ Sxx += (double) ptA.x * (double) ptB.x;
+ Sxy += (double) ptA.x * (double) ptB.y;
+ Sxz += (double) ptA.x * (double) ptB.z;
+ Syx += (double) ptA.y * (double) ptB.x;
+ Syy += (double) ptA.y * (double) ptB.y;
+ Syz += (double) ptA.y * (double) ptB.z;
+ Szx += (double) ptA.z * (double) ptB.x;
+ Szy += (double) ptA.z * (double) ptB.y;
+ Szz += (double) ptA.z * (double) ptB.z;
+ }
+ retStddev[0] = getRmsd(centerAndPoints, q);
+ double[][] N = new double[4][4];
+ N[0][0] = Sxx + Syy + Szz;
+ N[0][1] = N[1][0] = Syz - Szy;
+ N[0][2] = N[2][0] = Szx - Sxz;
+ N[0][3] = N[3][0] = Sxy - Syx;
+
+ N[1][1] = Sxx - Syy - Szz;
+ N[1][2] = N[2][1] = Sxy + Syx;
+ N[1][3] = N[3][1] = Szx + Sxz;
+
+ N[2][2] = -Sxx + Syy - Szz;
+ N[2][3] = N[3][2] = Syz + Szy;
+
+ N[3][3] = -Sxx - Syy + Szz;
+
+ // this construction prevents JavaScript from requiring preloading of Eigen
+
+ float[] v = ((EigenInterface) Interface.getInterface("javajs.util.Eigen"))
+ .setM(N).getEigenvectorsFloatTransposed()[3];
+ q = Quat.newP4(P4.new4(v[1], v[2], v[3], v[0]));
+ retStddev[1] = getRmsd(centerAndPoints, q);
+ return q;
+ }
+
+ /**
+ * Fills a 4x4 matrix with rotation-translation of mapped points A to B.
+ * If centerA is null, this is a standard 4x4 rotation-translation matrix;
+ * otherwise, this 4x4 matrix is a rotation around a vector through the center of ptsA,
+ * and centerA is filled with that center;
+ * Prior to Jmol 14.3.12_2014.02.14, when used from the JmolScript compare() function,
+ * this method returned the second of these options instead of the first.
+ *
+ * @param ptsA
+ * @param ptsB
+ * @param m 4x4 matrix to be returned
+ * @param centerA return center of rotation; if null, then standard 4x4 matrix is returned
+ * @return stdDev
+ */
+ public static float getTransformMatrix4(Lst<P3> ptsA, Lst<P3> ptsB, M4 m,
+ P3 centerA) {
+ P3[] cptsA = getCenterAndPoints(ptsA);
+ P3[] cptsB = getCenterAndPoints(ptsB);
+ float[] retStddev = new float[2];
+ Quat q = calculateQuaternionRotation(new P3[][] { cptsA, cptsB },
+ retStddev);
+ M3 r = q.getMatrix();
+ if (centerA == null)
+ r.rotate(cptsA[0]);
+ else
+ centerA.setT(cptsA[0]);
+ V3 t = V3.newVsub(cptsB[0], cptsA[0]);
+ m.setMV(r, t);
+ return retStddev[1];
+ }
+
+ /**
+ * from a list of points, create an array that includes the center
+ * point as the first point. This array is used as a starting point for
+ * a quaternion analysis of superposition.
+ *
+ * @param vPts
+ * @return array of points with first point center
+ */
+ public static P3[] getCenterAndPoints(Lst<P3> vPts) {
+ int n = vPts.size();
+ P3[] pts = new P3[n + 1];
+ pts[0] = new P3();
+ if (n > 0) {
+ for (int i = 0; i < n; i++) {
+ pts[0].add(pts[i + 1] = vPts.get(i));
+ }
+ pts[0].scale(1f / n);
+ }
+ return pts;
+ }
+
+ public static float getRmsd(P3[][] centerAndPoints, Quat q) {
+ double sum2 = 0;
+ P3[] ptsA = centerAndPoints[0];
+ P3[] ptsB = centerAndPoints[1];
+ P3 cA = ptsA[0];
+ P3 cB = ptsB[0];
+ int n = ptsA.length - 1;
+ P3 ptAnew = new P3();
+
+ for (int i = n + 1; --i >= 1;) {
+ ptAnew.sub2(ptsA[i], cA);
+ q.transform2(ptAnew, ptAnew).add(cB);
+ sum2 += ptAnew.distanceSquared(ptsB[i]);
+ }
+ return (float) Math.sqrt(sum2 / n);
+ }
+
+}
--- /dev/null
+package javajs.util;
+
+import java.util.Hashtable;
+import java.util.Map;
+
+import javajs.api.GenericBinaryDocumentReader;
+
+/**
+ * A simple MessagePack reader. See https://github.com/msgpack/msgpack/blob/master/spec.md
+ * with very few dependencies.
+ *
+ * Nuances:
+ *
+ * Does not implement unsigned int32 or int64 (delivers simple integers in all cases).
+ * Does not use doubles; just floats
+ *
+ * Note:
+ *
+ * homogeneousArrays == true will deliver null for empty array.
+ *
+ *
+ * Use in MMTF:
+ *
+ *
+ * BufferedInputStream bs = [whatever]
+ *
+ * GenericBinaryDocument binaryDoc = new javajs.util.BinaryDocument();
+ *
+ * binaryDoc.setStream(bs, true);
+ *
+ *
+ * map = (new MessagePackReader(binaryDoc, true)).readMap();
+ *
+ * entities = (Object[]) map.get("entityList");
+ *
+ * float[] x = (float[]) decode((byte[]) map.get("xCoordList"))
+ *
+ *
+ * @author Bob Hanson hansonr@stolaf.edu
+ */
+
+public class MessagePackReader {
+
+ private GenericBinaryDocumentReader doc;
+
+ private boolean isHomo;// homogeneous arrays -- use int[] not Integer
+
+ // these maps must be checked for the specific number of bits, in the following order:
+ private final static int POSITIVEFIXINT_x80 = 0x80; //0xxxxxxx
+ private final static int FIXMAP_xF0 = 0x80; //1000xxxx
+// private final static int FIXARRAY_xF0 = 0x90; //1001xxxx
+ private final static int FIXSTR_xE0 = 0xa0; //101xxxxx
+ private final static int NEGATIVEFIXINT_xE0 = 0xe0; //111xxxxx
+ private final static int DEFINITE_xE0 = 0xc0; //110xxxxx
+
+ private final static int NIL = 0xc0;
+// private final static int (NEVERUSED) = 0xc1;
+ private final static int FALSE = 0xc2;
+ private final static int TRUE = 0xc3;
+ private final static int BIN8 = 0xc4;
+ private final static int BIN16 = 0xc5;
+ private final static int BIN32 = 0xc6;
+ private final static int EXT8 = 0xc7;
+ private final static int EXT16 = 0xc8;
+ private final static int EXT32 = 0xc9;
+ private final static int FLOAT32 = 0xca;
+ private final static int FLOAT64 = 0xcb;
+ private final static int UINT8 = 0xcc;
+ private final static int UINT16 = 0xcd;
+ private final static int UINT32 = 0xce;
+ private final static int UINT64 = 0xcf;
+ private final static int INT8 = 0xd0;
+ private final static int INT16 = 0xd1;
+ private final static int INT32 = 0xd2;
+ private final static int INT64 = 0xd3;
+ private final static int FIXEXT1 = 0xd4;
+ private final static int FIXEXT2 = 0xd5;
+ private final static int FIXEXT4 = 0xd6;
+ private final static int FIXEXT8 = 0xd7;
+ private final static int FIXEXT16 = 0xd8;
+ private final static int STR8 = 0xd9;
+ private final static int STR16 = 0xda;
+ private final static int STR32 = 0xdb;
+ private final static int ARRAY16 = 0xdc;
+ private final static int ARRAY32 = 0xdd;
+ private final static int MAP16 = 0xde;
+ private final static int MAP32 = 0xdf;
+
+ public MessagePackReader(GenericBinaryDocumentReader binaryDoc, boolean isHomogeneousArrays) {
+ isHomo = isHomogeneousArrays;
+ doc = binaryDoc;
+ }
+
+ @SuppressWarnings("unchecked")
+ public Map<String, Object> readMap() throws Exception {
+ return (Map<String, Object>) getNext(null, 0);
+ }
+
+ public Object getNext(Object array, int pt) throws Exception {
+ int b = doc.readByte() & 0xFF;
+ int be0 = b & 0xE0;
+ if ((b & POSITIVEFIXINT_x80) == 0) {
+ if (array != null) {
+ ((int[]) array)[pt] = b;
+ return null;
+ }
+ return Integer.valueOf(b);
+ }
+ switch (be0) {
+ case NEGATIVEFIXINT_xE0:
+ b = BC.intToSignedInt(b | 0xFFFFFF00);
+ if (array != null) {
+ ((int[]) array)[pt] = b;
+ return null;
+ }
+ return Integer.valueOf(b);
+ case FIXSTR_xE0: {
+ String s = doc.readString(b & 0x1F);
+ if (array != null) {
+ ((String[]) array)[pt] = s;
+ return null;
+ }
+ return s;
+ }
+ case FIXMAP_xF0:
+ return ((b & 0xF0) == FIXMAP_xF0 ? getMap(b & 0x0F) : getArray(b & 0x0F));
+ case DEFINITE_xE0:
+ switch (b) {
+ case NIL:
+ return null;
+ case FALSE:
+ return Boolean.FALSE;
+ case TRUE:
+ return Boolean.TRUE;
+ case EXT8:
+ return getObject(doc.readUInt8());
+ case EXT16:
+ return getObject(doc.readUnsignedShort());
+ case EXT32:
+ return getObject(doc.readInt()); // should be unsigned int
+ case FIXEXT1:
+ return getObject(1);
+ case FIXEXT2:
+ return getObject(2);
+ case FIXEXT4:
+ return getObject(4);
+ case FIXEXT8:
+ return getObject(8);
+ case FIXEXT16:
+ return getObject(16);
+ case ARRAY16:
+ return getArray(doc.readUnsignedShort());
+ case ARRAY32:
+ return getArray(doc.readInt());
+ case MAP16:
+ return getMap(doc.readUnsignedShort());
+ case MAP32:
+ return getMap(doc.readInt());
+
+ // binary arrays:
+
+ case BIN8:
+ return doc.readBytes(doc.readUInt8());
+ case BIN16:
+ return doc.readBytes(doc.readUnsignedShort());
+ case BIN32:
+ return doc.readBytes(doc.readInt());
+ }
+ if (array == null) {
+ switch (b) {
+ case FLOAT32:
+ return Float.valueOf(doc.readFloat());
+ case FLOAT64:
+ return Float.valueOf((float) doc.readDouble());
+ case UINT8:
+ return Integer.valueOf(doc.readUInt8());
+ case UINT16:
+ return Integer.valueOf(doc.readUnsignedShort());
+ case UINT32:
+ return Integer.valueOf(doc.readInt()); // technically should be UInt32
+ case UINT64:
+ return Long.valueOf(doc.readLong()); // should be unsigned long; incompatible with JavaScript!
+ case INT8:
+ return Integer.valueOf(doc.readByte());
+ case INT16:
+ return Integer.valueOf(doc.readShort());
+ case INT32:
+ return Integer.valueOf(doc.readInt()); // should be Unsigned Int here
+ case INT64:
+ return Long.valueOf(doc.readLong());
+ case STR8:
+ return doc.readString(doc.readUInt8());
+ case STR16:
+ return doc.readString(doc.readShort());
+ case STR32:
+ return doc.readString(doc.readInt());
+ }
+ } else {
+ switch (b) {
+ case FLOAT32:
+ ((float[]) array)[pt] = doc.readFloat();
+ break;
+ case FLOAT64:
+ ((float[]) array)[pt] = (float) doc.readDouble();
+ break;
+ case UINT8:
+ ((int[]) array)[pt] = doc.readUInt8();
+ break;
+ case UINT16:
+ ((int[]) array)[pt] = doc.readUnsignedShort();
+ break;
+ case UINT32:
+ ((int[]) array)[pt] = doc.readInt(); // should be unsigned int
+ break;
+ case UINT64:
+ ((int[]) array)[pt] = (int) doc.readLong(); // should be unsigned long; incompatible with JavaScript!
+ break;
+ case INT8:
+ ((int[]) array)[pt] = doc.readByte();
+ break;
+ case INT16:
+ ((int[]) array)[pt] = doc.readShort();
+ break;
+ case INT32:
+ ((int[]) array)[pt] = doc.readInt(); // should be Unsigned Int here
+ break;
+ case INT64:
+ ((int[]) array)[pt] = (int) doc.readLong();
+ break;
+ case STR8:
+ ((String[]) array)[pt] = doc.readString(doc.readUInt8());
+ break;
+ case STR16:
+ ((String[]) array)[pt] = doc.readString(doc.readShort());
+ break;
+ case STR32:
+ ((String[]) array)[pt] = doc.readString(doc.readInt());
+ break;
+ }
+ }
+ }
+ return null;
+ }
+
+ private Object getObject(int n) throws Exception {
+ return new Object[] { Integer.valueOf(doc.readUInt8()), doc.readBytes(n) };
+ }
+
+ private Object getArray(int n) throws Exception {
+ if (isHomo) {
+ if (n == 0)
+ return null;
+ Object v = getNext(null, 0);
+ if (v instanceof Integer) {
+ int[] a = new int[n];
+ a[0] = ((Integer) v).intValue();
+ v = a;
+ } else if (v instanceof Float) {
+ float[] a = new float[n];
+ a[0] = ((Float) v).floatValue();
+ v = a;
+ } else if (v instanceof String) {
+ String[] a = new String[n];
+ a[0] = (String) v;
+ v = a;
+ } else {
+ Object[] o = new Object[n];
+ o[0] = v;
+ for (int i = 1; i < n; i++)
+ o[i] = getNext(null, 0);
+ return o;
+ }
+ for (int i = 1; i < n; i++)
+ getNext(v, i);
+ return v;
+ }
+ Object[] o = new Object[n];
+ for (int i = 0; i < n; i++)
+ o[i] = getNext(null, 0);
+ return o;
+ }
+
+ private Object getMap(int n) throws Exception {
+ Map<String, Object> map = new Hashtable<String, Object>();
+ for (int i = 0; i < n; i++) {
+ String key = getNext(null, 0).toString();
+ //Logger.info(key);
+
+ Object value = getNext(null, 0);
+ if (value == null) {
+ //Logger.info("null value for " + key);
+ } else {
+ map.put(key, value);
+ }
+ }
+ return map;
+ }
+
+ /////////////// MMTF MessagePack decoding ///////////////
+
+ /**
+ * This single method takes care of all MMTF needs.
+ *
+ * See https://github.com/rcsb/mmtf/blob/master/spec.md
+ *
+ * @param b
+ *
+ * @return array of int, char, or float, depending upon the type
+ */
+ public static Object decode(byte[] b) {
+ int type = BC.bytesToInt(b, 0, true);
+ int n = BC.bytesToInt(b, 4, true);
+ int param = BC.bytesToInt(b, 8, true);
+ switch (type) {
+ case 1:
+ return getFloats(b, n, 1);
+ case 2: // 1-byte
+ case 3: // 2-byte
+ case 4: // 4-byte
+ return getInts(b, n);
+ case 5:
+ return rldecode32ToStr(b);
+ case 6:
+ return rldecode32ToChar(b, n);
+ case 7:
+ return rldecode32(b, n);
+ case 8:
+ return rldecode32Delta(b, n);
+ case 9:
+ return rldecodef(b, n, param);
+ case 10:
+ return unpack16Deltaf(b, n, param);
+ case 11:
+ return getFloats(b, n, param);
+ case 12: // two-byte
+ case 13: // one-byte
+ return unpackf(b, 14 - type, n, param);
+ case 14: // two-byte
+ case 15: // one-byte
+ return unpack(b, 16 - type, n);
+ default:
+ System.out.println("MMTF type " + type + " not found!");
+ return null;
+ }
+ }
+
+ /**
+ * mmtf type 1 and 11
+ *
+ * byte[4] to float32
+ *
+ * @param b
+ * @param n
+ * @param divisor
+ * @return array of floats
+ */
+ public static float[] getFloats(byte[] b, int n, float divisor) {
+ if (b == null)
+ return null;
+ float[] a = new float[n];
+ try {
+ switch ((b.length - 12) / n) {
+ case 2:
+ for (int i = 0, j = 12; i < n; i++, j += 2)
+ a[i] = BC.bytesToShort(b, j, false) / divisor;
+ break;
+ case 4:
+ for (int i = 0, j = 12; i < n; i++, j += 4)
+ a[i] = BC.bytesToFloat(b, j, false);
+ break;
+ }
+ } catch (Exception e) {
+ }
+ return a;
+ }
+
+ /**
+ * mmtf types 2-4
+ *
+ * Decode a byte array into a byte, short, or int array.
+ *
+ * @param b
+ * @param n
+ *
+ * @return array of integers
+ */
+ public static int[] getInts(byte[] b, int n) {
+ if (b == null)
+ return null;
+ int[] a = new int[n];
+ switch ((b.length - 12) / n) {
+ case 1:
+ for (int i = 0, j = 12; i < n; i++, j++)
+ a[i] = b[j];
+ break;
+ case 2:
+ for (int i = 0, j = 12; i < n; i++, j += 2)
+ a[i] = BC.bytesToShort(b, j, true);
+ break;
+ case 4:
+ for (int i = 0, j = 12; i < n; i++, j += 4)
+ a[i] = BC.bytesToInt(b, j, true);
+ break;
+ }
+ return a;
+ }
+
+ /**
+ * mmtf type 5
+ *
+ * Decode each four bytes as a 1- to 4-character string label where a 0 byte
+ * indicates end-of-string.
+ *
+ * @param b
+ * a byte array
+ * @return String[]
+ */
+ public static String[] rldecode32ToStr(byte[] b) {
+ String[] id = new String[(b.length - 12) / 4];
+ out: for (int i = 0, len = id.length, pt = 12; i < len; i++) {
+ SB sb = new SB();
+ for (int j = 0; j < 4; j++) {
+ switch (b[pt]) {
+ case 0:
+ id[i] = sb.toString();
+ pt += 4 - j;
+ continue out;
+ default:
+ sb.appendC((char) b[pt++]);
+ if (j == 3)
+ id[i] = sb.toString();
+ continue;
+ }
+ }
+ }
+ return id;
+ }
+
+ /**
+ * mmtf type 6
+ *
+ * Decode an array of int32 using run-length decoding to one char per int.
+ *
+ * @param b
+ * @param n
+ * @return array of characters
+ */
+ public static char[] rldecode32ToChar(byte[] b, int n) {
+ if (b == null)
+ return null;
+ char[] ret = new char[n];
+ for (int i = 0, pt = 3; i < n;) {
+ char val = (char) b[((pt++) << 2) + 3];
+ for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
+ ret[i++] = val;
+ }
+ return ret;
+ }
+
+ /**
+ * mmtf type 7
+ *
+ * Decode an array of int32 using run-length decoding.
+ *
+ * @param b
+ * @param n
+ * @return array of integers
+ */
+ public static int[] rldecode32(byte[] b, int n) {
+ if (b == null)
+ return null;
+ int[] ret = new int[n];
+ for (int i = 0, pt = 3; i < n;) {
+ int val = BC.bytesToInt(b, (pt++) << 2, true);
+ for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
+ ret[i++] = val;
+ }
+ return ret;
+ }
+
+ /**
+ * mmtf type 8
+ *
+ * Decode an array of int32 using run-length decoding of a difference array.
+ *
+ * @param b
+ * @param n
+ * @return array of integers
+ */
+ public static int[] rldecode32Delta(byte[] b, int n) {
+ if (b == null)
+ return null;
+ int[] ret = new int[n];
+ for (int i = 0, pt = 3, val = 0; i < n;) {
+ int diff = BC.bytesToInt(b, (pt++) << 2, true);
+ for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
+ ret[i++] = (val = val + diff);
+ }
+ return ret;
+ }
+
+ /**
+ * mmtf type 9
+ *
+ * Decode an array of int32 using run-length decoding and divide by a divisor
+ * to give a float32.
+ *
+ * @param b
+ * @param n
+ * @param divisor
+ * @return array of floats
+ */
+ public static float[] rldecodef(byte[] b, int n, float divisor) {
+ if (b == null)
+ return null;
+ float[] ret = new float[n];
+ for (int i = 0, pt = 3; i < n;) {
+ int val = BC.bytesToInt(b, (pt++) << 2, true);
+ for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
+ ret[i++] = val / divisor;
+ }
+ return ret;
+ }
+
+ /**
+ *
+ * mmtf type 10
+ *
+ * Decode an array of int16 using run-length decoding of a difference array.
+ *
+ * @param b
+ * @param n
+ * @param divisor
+ * @return array of floats
+ */
+ public static float[] unpack16Deltaf(byte[] b, int n, float divisor) {
+ if (b == null)
+ return null;
+ float[] ret = new float[n];
+ for (int i = 0, pt = 6, val = 0, buf = 0; i < n;) {
+ int diff = BC.bytesToShort(b, (pt++) << 1, true);
+ if (diff == Short.MAX_VALUE || diff == Short.MIN_VALUE) {
+ buf += diff;
+ } else {
+ ret[i++] = (val = val + diff + buf) / divisor;
+ buf = 0;
+ }
+ }
+ return ret;
+ }
+
+ /**
+ *
+ * mmtf type 12 and 13
+ *
+ * Unpack an array of int8 or int16 to int32 and divide to give a float32.
+ *
+ * untested
+ *
+ * @param b
+ * @param nBytes
+ * @param n
+ * @param divisor
+ * @return array of floats
+ */
+ public static float[] unpackf(byte[] b, int nBytes, int n, float divisor) {
+ if (b == null)
+ return null;
+ float[] ret = new float[n];
+ switch (nBytes) {
+ case 1:
+ for (int i = 0, pt = 12, offset = 0; i < n;) {
+ int val = b[pt++];
+ if (val == Byte.MAX_VALUE || val == Byte.MIN_VALUE) {
+ offset += val;
+ } else {
+ ret[i++] = (val + offset) / divisor;
+ offset = 0;
+ }
+ }
+ break;
+ case 2:
+ for (int i = 0, pt = 6, offset = 0; i < n;) {
+ int val = BC.bytesToShort(b, (pt++) << 1, true);
+ if (val == Short.MAX_VALUE || val == Short.MIN_VALUE) {
+ offset += val;
+ } else {
+ ret[i++] = (val + offset) / divisor;
+ offset = 0;
+ }
+ }
+ break;
+ }
+ return ret;
+ }
+
+ /**
+ *
+ * mmtf type 14 and 15
+ *
+ * Unpack an array of int8 or int16 to int32.
+ *
+ * untested
+ *
+ * @param b
+ * @param nBytes
+ * @param n
+ * @return array of integers
+ */
+ public static int[] unpack(byte[] b, int nBytes, int n) {
+ if (b == null)
+ return null;
+ int[] ret = new int[n];
+ switch (nBytes) {
+ case 1:
+ for (int i = 0, pt = 12, offset = 0; i < n;) {
+ int val = b[pt++];
+ if (val == Byte.MAX_VALUE || val == Byte.MIN_VALUE) {
+ offset += val;
+ } else {
+ ret[i++] = val + offset;
+ offset = 0;
+ }
+ }
+ break;
+ case 2:
+ for (int i = 0, pt = 6, offset = 0; i < n;) {
+ int val = BC.bytesToShort(b, (pt++) << 1, true);
+ if (val == Short.MAX_VALUE || val == Short.MIN_VALUE) {
+ offset += val;
+ } else {
+ ret[i++] = val + offset;
+ offset = 0;
+ }
+ }
+ break;
+ }
+ return ret;
+ }
+
+ ///**
+ //* Decode an array of int16 using run-length decoding
+ //* of a difference array.
+ //*
+ //* @param b
+ //* @param n
+ //* @param i0
+ //* @return array of integers
+ //*/
+ //public static int[] rldecode16Delta(byte[] b, int n, int i0) {
+ //if (b == null)
+ //return null;
+ //int[] ret = new int[n];
+ //for (int i = 0, pt = i0 / 2, val = 0; i < n;) {
+ //int diff = BC.bytesToShort(b, (pt++) << 1, true);
+ //for (int j = BC.bytesToShort(b, (pt++) << 1, true); --j >= 0;)
+ //ret[i++] = (val = val + diff);
+ //}
+ //return ret;
+ //}
+
+ ///**
+ //* Do a split delta to a float[] array
+ //* @param xyz label "x", "y", "z", or "bFactor"
+ //* @param factor for dividing in the end -- 1000f or 100f
+ //* @return float[]
+ //*
+ //*/
+ //public static float[] getFloatsSplit(String xyz, float factor) {
+ //byte[] big = (byte[]) map.get(xyz + "Big");
+ //return (big == null ? null : splitDelta(big,
+ //(byte[]) map.get(xyz + "Small"), fileAtomCount, factor));
+ //}
+
+ ///**
+ //* Do a split delta to a float[] array
+ //*
+ //* @param big
+ //* [n m n m n m...] where n is a "big delta" and m is a number of
+ //* "small deltas
+ //* @param small
+ //* array containing the small deltas
+ //* @param n
+ //* the size of the final array
+ //* @param factor
+ //* to divide the final result by -- 1000f or 100f here
+ //* @return float[]
+ //*/
+ //public static float[] splitDelta(byte[] big, byte[] small, int n, float factor) {
+ //float[] ret = new float[n];
+ //for (int i = 0, smallpt = 0, val = 0, datapt = 0, len = big.length >> 2; i < len; i++) {
+ //ret[datapt++] = (val = val + BC.bytesToInt(big, i << 2, true)) / factor;
+ //if (++i < len)
+ //for (int j = BC.bytesToInt(big, i << 2, true); --j >= 0; smallpt++)
+ //ret[datapt++] = (val = val + BC.bytesToShort(small, smallpt << 1, true))
+ // / factor;
+ //}
+ //return ret;
+ //}
+ //
+
+
+}
--- /dev/null
+package javajs.util;
+
+import java.io.BufferedWriter;
+import java.io.ByteArrayOutputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+import javajs.J2SIgnoreImport;
+import javajs.api.BytePoster;
+import javajs.api.GenericOutputChannel;
+import javajs.api.js.J2SObjectInterface;
+
+/**
+ *
+ * A generic output method. JmolOutputChannel can be used to:
+ *
+ * add characters to a StringBuffer
+ * using fileName==null, append() and toString()
+ *
+ * add bytes utilizing ByteArrayOutputStream
+ * using writeBytes(), writeByteAsInt(), append()*, and bytesAsArray()
+ * *append() can be used as long as os==ByteArrayOutputStream
+ * or it is not used before one of the writeByte methods.
+ *
+ * output characters to a FileOutputStream
+ * using os==FileOutputStream, asWriter==true, append(), and closeChannel()
+ *
+ * output bytes to a FileOutputStream
+ * using os==FileOutputStream, writeBytes(), writeByteAsInt(), append(), and closeChannel()
+ *
+ * post characters or bytes to a remote server
+ * using fileName=="http://..." or "https://...",
+ * writeBytes(), writeByteAsInt(), append(), and closeChannel()
+ *
+ * send characters or bytes to a JavaScript function
+ * when JavaScript and (typeof fileName == "function")
+ *
+ * if fileName equals ";base64,", then the data are base64-encoded
+ * prior to writing, and closeChannel() returns the data.
+ *
+ * @author hansonr Bob Hanson hansonr@stolaf.edu 9/2013
+ *
+ *
+ */
+
+@J2SIgnoreImport({ java.io.FileOutputStream.class })
+public class OC extends OutputStream implements GenericOutputChannel {
+
+ private BytePoster bytePoster; // only necessary for writing to http:// or https://
+ private String fileName;
+ private BufferedWriter bw;
+ private boolean isLocalFile;
+ private int byteCount;
+ private boolean isCanceled;
+ private boolean closed;
+ private OutputStream os;
+ private SB sb;
+ private String type;
+ private boolean isBase64;
+ private OutputStream os0;
+ private byte[] bytes; // preset bytes; output only
+
+ public boolean bigEndian = true;
+
+ @Override
+ public boolean isBigEndian() {
+ return bigEndian;
+ }
+
+ public void setBigEndian(boolean TF) {
+ bigEndian = TF;
+ }
+
+ public OC setParams(BytePoster bytePoster, String fileName,
+ boolean asWriter, OutputStream os) {
+ this.bytePoster = bytePoster;
+ isBase64 = ";base64,".equals(fileName);
+ if (isBase64) {
+ fileName = null;
+ os0 = os;
+ os = null;
+ }
+ this.fileName = fileName;
+ this.os = os;
+ isLocalFile = (fileName != null && !isRemote(fileName));
+ if (asWriter && !isBase64 && os != null)
+ bw = Rdr.getBufferedWriter(os, null);
+ return this;
+ }
+
+ public OC setBytes(byte[] b) {
+ bytes = b;
+ return this;
+ }
+
+ public String getFileName() {
+ return fileName;
+ }
+
+ public String getName() {
+ return (fileName == null ? null : fileName.substring(fileName.lastIndexOf("/") + 1));
+ }
+
+ public int getByteCount() {
+ return byteCount;
+ }
+
+ /**
+ *
+ * @param type user-identified type (PNG, JPG, etc)
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * will go to string buffer if bw == null and os == null
+ *
+ * @param s
+ * @return this, for chaining like a standard StringBuffer
+ *
+ */
+ public OC append(String s) {
+ try {
+ if (bw != null) {
+ bw.write(s);
+ } else if (os == null) {
+ if (sb == null)
+ sb = new SB();
+ sb.append(s);
+ } else {
+ byte[] b = s.getBytes();
+ os.write(b, 0, b.length);
+ byteCount += b.length;
+ return this;
+ }
+ } catch (IOException e) {
+ // ignore
+ }
+ byteCount += s.length(); // not necessarily exactly correct if unicode
+ return this;
+ }
+
+ @Override
+ public void reset() {
+ sb = null;
+ initOS();
+ }
+
+
+ private void initOS() {
+ if (sb != null) {
+ String s = sb.toString();
+ reset();
+ append(s);
+ return;
+ }
+ try {
+ /**
+ * @j2sNative
+ *
+ * this.os = null;
+ */
+ {
+ if (os instanceof FileOutputStream) {
+ os.close();
+ os = new FileOutputStream(fileName);
+ } else {
+ os = null;
+ }
+ }
+ if (os == null)
+ os = new ByteArrayOutputStream();
+ if (bw != null) {
+ bw.close();
+ bw = Rdr.getBufferedWriter(os, null);
+ }
+ } catch (Exception e) {
+ // not perfect here.
+ System.out.println(e.toString());
+ }
+ byteCount = 0;
+ }
+
+ /**
+ * @param b
+ */
+ @Override
+ public void writeByteAsInt(int b) {
+ if (os == null)
+ initOS();
+ {
+ try {
+ os.write(b);
+ } catch (IOException e) {
+ }
+ }
+ byteCount++;
+ }
+
+ @Override
+ public void write(byte[] buf, int i, int len) {
+ if (os == null)
+ initOS();
+ try {
+ os.write(buf, i, len);
+ } catch (IOException e) {
+ }
+ byteCount += len;
+ }
+
+ @Override
+ public void writeShort(short i) {
+ if (isBigEndian()) {
+ writeByteAsInt(i >> 8);
+ writeByteAsInt(i);
+ } else {
+ writeByteAsInt(i);
+ writeByteAsInt(i >> 8);
+ }
+ }
+
+ @Override
+ public void writeLong(long b) {
+ if (isBigEndian()) {
+ writeInt((int) ((b >> 32) & 0xFFFFFFFFl));
+ writeInt((int) (b & 0xFFFFFFFFl));
+ } else {
+ writeByteAsInt((int) (b >> 56));
+ writeByteAsInt((int) (b >> 48));
+ writeByteAsInt((int) (b >> 40));
+ writeByteAsInt((int) (b >> 32));
+ writeByteAsInt((int) (b >> 24));
+ writeByteAsInt((int) (b >> 16));
+ writeByteAsInt((int) (b >> 8));
+ writeByteAsInt((int) b);
+ }
+ }
+
+ public void write(int b) {
+ // required by standard ZipOutputStream -- do not use, as it will break JavaScript methods
+ if (os == null)
+ initOS();
+ try {
+ os.write(b);
+ } catch (IOException e) {
+ }
+ byteCount++;
+ }
+
+ public void write(byte[] b) {
+ // not used in JavaScript due to overloading problem there
+ write(b, 0, b.length);
+ }
+
+ public void cancel() {
+ isCanceled = true;
+ closeChannel();
+ }
+
+ @Override
+ @SuppressWarnings({ "unused" })
+ public String closeChannel() {
+ if (closed)
+ return null;
+ // can't cancel file writers
+ try {
+ if (bw != null) {
+ bw.flush();
+ bw.close();
+ } else if (os != null) {
+ os.flush();
+ os.close();
+ }
+ if (os0 != null && isCanceled) {
+ os0.flush();
+ os0.close();
+ }
+ } catch (Exception e) {
+ // ignore closing issues
+ }
+ if (isCanceled) {
+ closed = true;
+ return null;
+ }
+ if (fileName == null) {
+ if (isBase64) {
+ String s = getBase64();
+ if (os0 != null) {
+ os = os0;
+ append(s);
+ }
+ sb = new SB();
+ sb.append(s);
+ isBase64 = false;
+ return closeChannel();
+ }
+ return (sb == null ? null : sb.toString());
+ }
+ closed = true;
+ J2SObjectInterface jmol = null;
+ Object _function = null;
+ /**
+ * @j2sNative
+ *
+ * jmol = self.J2S || Jmol; _function = (typeof this.fileName == "function" ?
+ * this.fileName : null);
+ *
+ */
+ {
+ if (!isLocalFile) {
+ String ret = postByteArray(); // unsigned applet could do this
+ if (ret.startsWith("java.net"))
+ byteCount = -1;
+ return ret;
+ }
+ }
+ if (jmol != null) {
+ Object data = (sb == null ? toByteArray() : sb.toString());
+ if (_function == null)
+ jmol._doAjax(fileName, null, data, sb == null);
+ else
+ jmol._apply(_function, data);
+ }
+ return null;
+ }
+
+ public boolean isBase64() {
+ return isBase64;
+ }
+
+ public String getBase64() {
+ return Base64.getBase64(toByteArray()).toString();
+ }
+
+ public byte[] toByteArray() {
+ return (bytes != null ? bytes : os instanceof ByteArrayOutputStream ? ((ByteArrayOutputStream)os).toByteArray() : null);
+ }
+
+ @Override
+ @Deprecated
+ public void close() {
+ closeChannel();
+ }
+
+ @Override
+ public String toString() {
+ if (bw != null)
+ try {
+ bw.flush();
+ } catch (IOException e) {
+ // TODO
+ }
+ if (sb != null)
+ return closeChannel();
+ return byteCount + " bytes";
+ }
+
+ private String postByteArray() {
+ byte[] bytes = (sb == null ? toByteArray() : sb.toString().getBytes());
+ return bytePoster.postByteArray(fileName, bytes);
+ }
+
+ public final static String[] urlPrefixes = { "http:", "https:", "sftp:", "ftp:",
+ "file:" };
+ // note that SFTP is not supported
+ public final static int URL_LOCAL = 4;
+
+ public static boolean isRemote(String fileName) {
+ if (fileName == null)
+ return false;
+ int itype = urlTypeIndex(fileName);
+ return (itype >= 0 && itype != URL_LOCAL);
+ }
+
+ public static boolean isLocal(String fileName) {
+ if (fileName == null)
+ return false;
+ int itype = urlTypeIndex(fileName);
+ return (itype < 0 || itype == URL_LOCAL);
+ }
+
+ public static int urlTypeIndex(String name) {
+ if (name == null)
+ return -2; // local unsigned applet
+ for (int i = 0; i < urlPrefixes.length; ++i) {
+ if (name.startsWith(urlPrefixes[i])) {
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ @Override
+ public void writeInt(int i) {
+ if (bigEndian) {
+ writeByteAsInt(i >> 24);
+ writeByteAsInt(i >> 16);
+ writeByteAsInt(i >> 8);
+ writeByteAsInt(i);
+ } else {
+ writeByteAsInt(i);
+ writeByteAsInt(i >> 8);
+ writeByteAsInt(i >> 16);
+ writeByteAsInt(i >> 24);
+ }
+ }
+
+ public void writeFloat(float x) {
+ writeInt(x == 0 ? 0 : Float.floatToIntBits(x));
+ }
+
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+
+
+/**
+ * A 3 element point that is represented by single precision floating point
+ * x,y,z coordinates.
+ *
+ * @version specification 1.1, implementation $Revision: 1.10 $, $Date:
+ * 2006/09/08 20:20:20 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012
+ * for unique constructor and method names
+ * for the optimization of compiled JavaScript using Java2Script.
+ *
+ *
+ */
+public class P3 extends T3 {
+
+ public static P3 newP(T3 t) {
+ P3 p = new P3();
+ p.x = t.x;
+ p.y = t.y;
+ p.z = t.z;
+ return p;
+ }
+
+ private static P3 unlikely;
+
+ public static P3 getUnlikely() {
+ return (unlikely == null ? unlikely = new3((float) Math.PI, (float) Math.E, (float) (Math.PI * Math.E)) : unlikely);
+ }
+
+ public static P3 new3(float x, float y, float z) {
+ P3 p = new P3();
+ p.x = x;
+ p.y = y;
+ p.z = z;
+ return p;
+ }
+
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+
+
+/**
+ * A 3 element point that is represented by signed integer x,y,z coordinates.
+ *
+ * @since Java 3D 1.2
+ * @version specification 1.2, implementation $Revision: 1.9 $, $Date:
+ * 2006/07/28 17:01:33 $
+ * @author Kenji hiranabe
+ *
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012 for unique
+ * constructor and method names for the optimization of compiled
+ * JavaScript using Java2Script.
+ *
+ */
+public class P3i extends T3i {
+
+ public static P3i new3(int x, int y, int z) {
+ P3i pt = new P3i();
+ pt.x = x;
+ pt.y = y;
+ pt.z = z;
+ return pt;
+ }
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+
+
+/**
+ * A 4 element point that is represented by single precision floating point
+ * x,y,z,w coordinates.
+ *
+ * @version specification 1.1, implementation $Revision: 1.9 $, $Date:
+ * 2006/07/28 17:01:32 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012
+ * for unique constructor and method names
+ * for the optimization of compiled JavaScript using Java2Script.
+ *
+ */
+public class P4 extends T4 {
+
+ public static P4 new4(float x, float y, float z, float w) {
+ P4 pt = new P4();
+ pt.set4(x, y, z, w);
+ return pt;
+ }
+
+ public static P4 newPt(P4 value) {
+ P4 pt = new P4();
+ pt.set4(value.x, value.y, value.z, value.w);
+ return pt;
+ }
+
+ /**
+ * Returns the distance between this point and point p1.
+ *
+ * @param p1
+ * the other point
+ * @return the distance between these two points
+ */
+ public final float distance4(P4 p1) {
+ double dx = x - p1.x;
+ double dy = y - p1.y;
+ double dz = z - p1.z;
+ double dw = w - p1.w;
+ return (float) Math.sqrt(dx * dx + dy * dy + dz * dz + dw * dw);
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-04-26 16:57:51 -0500 (Thu, 26 Apr 2007) $
+ * $Revision: 7502 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.util;
+
+import java.lang.reflect.Array;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javajs.J2SIgnoreImport;
+import javajs.api.JSONEncodable;
+
+/**
+ * a combination of Parsing and Text-related utility classes
+ *
+ * @author hansonr
+ *
+ */
+
+@J2SIgnoreImport(value = { java.lang.reflect.Array.class })
+public class PT {
+
+ public static int parseInt(String str) {
+ return parseIntNext(str, new int[] {0});
+ }
+
+ public static int parseIntNext(String str, int[] next) {
+ int cch = str.length();
+ if (next[0] < 0 || next[0] >= cch)
+ return Integer.MIN_VALUE;
+ return parseIntChecked(str, cch, next);
+ }
+
+ public static int parseIntChecked(String str, int ichMax, int[] next) {
+ boolean digitSeen = false;
+ int value = 0;
+ int ich = next[0];
+ if (ich < 0)
+ return Integer.MIN_VALUE;
+ int ch;
+ while (ich < ichMax && isWhiteSpace(str, ich))
+ ++ich;
+ boolean negative = false;
+ if (ich < ichMax && str.charAt(ich) == 45) { //"-"
+ negative = true;
+ ++ich;
+ }
+ while (ich < ichMax && (ch = str.charAt(ich)) >= 48 && ch <= 57) {
+ value = value * 10 + (ch - 48);
+ digitSeen = true;
+ ++ich;
+ }
+ if (!digitSeen)// || !checkTrailingText(str, ich, ichMax))
+ value = Integer.MIN_VALUE;
+ else if (negative)
+ value = -value;
+ next[0] = ich;
+ return value;
+ }
+
+ public static boolean isWhiteSpace(String str, int ich) {
+ char ch;
+ return (ich >= 0 && ((ch = str.charAt(ich)) == ' ' || ch == '\t' || ch == '\n'));
+ }
+
+ /**
+ * A float parser that is 30% faster than Float.parseFloat(x) and also accepts
+ * x.yD+-n
+ *
+ * @param str
+ * @param ichMax
+ * @param next
+ * pointer; incremented
+ * @param isStrict
+ * @return value or Float.NaN
+ */
+ public static float parseFloatChecked(String str, int ichMax, int[] next,
+ boolean isStrict) {
+ boolean digitSeen = false;
+ int ich = next[0];
+ if (isStrict && str.indexOf('\n') != str.lastIndexOf('\n'))
+ return Float.NaN;
+ while (ich < ichMax && isWhiteSpace(str, ich))
+ ++ich;
+ boolean negative = false;
+ if (ich < ichMax && str.charAt(ich) == '-') {
+ ++ich;
+ negative = true;
+ }
+ // looks crazy, but if we don't do this, Google Closure Compiler will
+ // write code that Safari will misinterpret in a VERY nasty way --
+ // getting totally confused as to long integers and double values
+
+ // This is Safari figuring out the values of the numbers on the line (x, y, then z):
+
+ // ATOM 1241 CD1 LEU A 64 -2.206 36.532 31.576 1.00 60.60 C
+ // e=1408749273
+ // -e =-1408749273
+ // ATOM 1241 CD1 LEU A 64 -2.206 36.532 31.576 1.00 60.60 C
+ // e=-1821066134
+ // e=36.532
+ // ATOM 1241 CD1 LEU A 64 -2.206 36.532 31.576 1.00 60.60 C
+ // e=-1133871366
+ // e=31.576
+ //
+ // "e" values are just before and after the "value = -value" statement.
+
+ int ch = 0;
+ float ival = 0f;
+ float ival2 = 0f;
+ while (ich < ichMax && (ch = str.charAt(ich)) >= 48 && ch <= 57) {
+ ival = (ival * 10f) + (ch - 48)*1f;
+ ++ich;
+ digitSeen = true;
+ }
+ boolean isDecimal = false;
+ int iscale = 0;
+ int nzero = (ival == 0 ? -1 : 0);
+ if (ch == '.') {
+ isDecimal = true;
+ while (++ich < ichMax && (ch = str.charAt(ich)) >= 48 && ch <= 57) {
+ digitSeen = true;
+ if (nzero < 0) {
+ if (ch == 48) {
+ nzero--;
+ continue;
+ }
+ nzero = -nzero;
+ }
+ if (iscale < decimalScale.length) {
+ ival2 = (ival2 * 10f) + (ch - 48)*1f;
+ iscale++;
+ }
+ }
+ }
+ float value;
+
+ // Safari breaks here intermittently converting integers to floats
+
+ if (!digitSeen) {
+ value = Float.NaN;
+ } else if (ival2 > 0) {
+ value = ival2 * decimalScale[iscale - 1];
+ if (nzero > 1) {
+ if (nzero - 2 < decimalScale.length) {
+ value *= decimalScale[nzero - 2];
+ } else {
+ value *= Math.pow(10, 1 - nzero);
+ }
+ } else {
+ value += ival;
+ }
+ } else {
+ value = ival;
+ }
+ boolean isExponent = false;
+ if (ich < ichMax && (ch == 69 || ch == 101 || ch == 68)) { // E e D
+ isExponent = true;
+ if (++ich >= ichMax)
+ return Float.NaN;
+ ch = str.charAt(ich);
+ if ((ch == '+') && (++ich >= ichMax))
+ return Float.NaN;
+ next[0] = ich;
+ int exponent = parseIntChecked(str, ichMax, next);
+ if (exponent == Integer.MIN_VALUE)
+ return Float.NaN;
+ if (exponent > 0 && exponent <= tensScale.length)
+ value *= tensScale[exponent - 1];
+ else if (exponent < 0 && -exponent <= decimalScale.length)
+ value *= decimalScale[-exponent - 1];
+ else if (exponent != 0)
+ value *= Math.pow(10, exponent);
+ } else {
+ next[0] = ich; // the exponent code finds its own ichNextParse
+ }
+ // believe it or not, Safari reports the long-equivalent of the
+ // float value here, then later the float value, after no operation!
+ if (negative)
+ value = -value;
+ if (value == Float.POSITIVE_INFINITY)
+ value = Float.MAX_VALUE;
+ return (!isStrict || (!isExponent || isDecimal)
+ && checkTrailingText(str, next[0], ichMax) ? value : Float.NaN);
+ }
+
+ public final static float[] tensScale = { 10f, 100f, 1000f, 10000f, 100000f, 1000000f };
+ public final static float[] decimalScale = {
+ 0.1f,
+ 0.01f,
+ 0.001f,
+ 0.0001f,
+ 0.00001f,
+ 0.000001f,
+ 0.0000001f,
+ 0.00000001f,
+ 0.000000001f
+ };
+ public static boolean checkTrailingText(String str, int ich, int ichMax) {
+ //number must be pure -- no additional characters other than white space or ;
+ char ch;
+ while (ich < ichMax && (isWhitespace(ch = str.charAt(ich)) || ch == ';'))
+ ++ich;
+ return (ich == ichMax);
+ }
+
+ public static float[] parseFloatArray(String str) {
+ return parseFloatArrayNext(str, new int[1], null, null, null);
+ }
+
+ public static int parseFloatArrayInfested(String[] tokens, float[] data) {
+ int len = data.length;
+ int nTokens = tokens.length;
+ int n = 0;
+ int max = 0;
+ for (int i = 0; i >= 0 && i < len && n < nTokens; i++) {
+ float f;
+ while (Float.isNaN(f = parseFloat(tokens[n++]))
+ && n < nTokens) {
+ }
+ if (!Float.isNaN(f))
+ data[(max = i)] = f;
+ if (n == nTokens)
+ break;
+ }
+ return max + 1;
+ }
+
+ /**
+ * @param str
+ * @param next
+ * @param f
+ * @param strStart or null
+ * @param strEnd or null
+ * @return array of float values
+ *
+ */
+ public static float[] parseFloatArrayNext(String str, int[] next, float[] f,
+ String strStart, String strEnd) {
+ int n = 0;
+ int pt = next[0];
+ if (pt >= 0) {
+ if (strStart != null) {
+ int p = str.indexOf(strStart, pt);
+ if (p >= 0)
+ next[0] = p + strStart.length();
+ }
+ str = str.substring(next[0]);
+ pt = (strEnd == null ? -1 : str.indexOf(strEnd));
+ if (pt < 0)
+ pt = str.length();
+ else
+ str = str.substring(0, pt);
+ next[0] += pt + 1;
+ String[] tokens = getTokens(str);
+ if (f == null)
+ f = new float[tokens.length];
+ n = parseFloatArrayInfested(tokens, f);
+ }
+ if (f == null)
+ return new float[0];
+ for (int i = n; i < f.length; i++)
+ f[i] = Float.NaN;
+ return f;
+ }
+
+ public static float parseFloatRange(String str, int ichMax, int[] next) {
+ int cch = str.length();
+ if (ichMax > cch)
+ ichMax = cch;
+ if (next[0] < 0 || next[0] >= ichMax)
+ return Float.NaN;
+ return parseFloatChecked(str, ichMax, next, false);
+ }
+
+ public static float parseFloatNext(String str, int[] next) {
+ int cch = (str == null ? -1 : str.length());
+ return (next[0] < 0 || next[0] >= cch ? Float.NaN : parseFloatChecked(str, cch, next, false));
+ }
+
+ public static float parseFloatStrict(String str) {
+ // checks trailing characters and does not allow "1E35" to be float
+ int cch = str.length();
+ if (cch == 0)
+ return Float.NaN;
+ return parseFloatChecked(str, cch, new int[] {0}, true);
+ }
+
+ public static float parseFloat(String str) {
+ return parseFloatNext(str, new int[] {0});
+ }
+
+ public static int parseIntRadix(String s, int i) throws NumberFormatException {
+ /**
+ *
+ * JavaScript uses parseIntRadix
+ *
+ * @j2sNative
+ *
+ * return Integer.parseIntRadix(s, i);
+ *
+ */
+ {
+ return Integer.parseInt(s, i);
+ }
+ }
+
+ public static String[] getTokens(String line) {
+ return getTokensAt(line, 0);
+ }
+
+ public static String parseToken(String str) {
+ return parseTokenNext(str, new int[] {0});
+ }
+
+ public static String parseTrimmed(String str) {
+ return parseTrimmedRange(str, 0, str.length());
+ }
+
+ public static String parseTrimmedAt(String str, int ichStart) {
+ return parseTrimmedRange(str, ichStart, str.length());
+ }
+
+ public static String parseTrimmedRange(String str, int ichStart, int ichMax) {
+ int cch = str.length();
+ if (ichMax < cch)
+ cch = ichMax;
+ if (cch < ichStart)
+ return "";
+ return parseTrimmedChecked(str, ichStart, cch);
+ }
+
+ public static String[] getTokensAt(String line, int ich) {
+ if (line == null)
+ return null;
+ int cchLine = line.length();
+ if (ich < 0 || ich > cchLine)
+ return null;
+ int tokenCount = countTokens(line, ich);
+ String[] tokens = new String[tokenCount];
+ int[] next = new int[1];
+ next[0] = ich;
+ for (int i = 0; i < tokenCount; ++i)
+ tokens[i] = parseTokenChecked(line, cchLine, next);
+ return tokens;
+ }
+
+ public static int countChar(String line, char c) {
+ int n = 0;
+ for (int i = line.lastIndexOf(c) + 1; --i >= 0;)
+ if (line.charAt(i) == c)
+ n++;
+ return n;
+ }
+
+ public static int countTokens(String line, int ich) {
+ int tokenCount = 0;
+ if (line != null) {
+ int ichMax = line.length();
+ while (true) {
+ while (ich < ichMax && isWhiteSpace(line, ich))
+ ++ich;
+ if (ich == ichMax)
+ break;
+ ++tokenCount;
+ do {
+ ++ich;
+ } while (ich < ichMax && !isWhiteSpace(line, ich));
+ }
+ }
+ return tokenCount;
+ }
+
+ public static String parseTokenNext(String str, int[] next) {
+ int cch = str.length();
+ return (next[0] < 0 || next[0] >= cch ? null : parseTokenChecked(str, cch, next));
+ }
+
+ public static String parseTokenRange(String str, int ichMax, int[] next) {
+ int cch = str.length();
+ if (ichMax > cch)
+ ichMax = cch;
+ return (next[0] < 0 || next[0] >= ichMax ? null : parseTokenChecked(str, ichMax, next));
+ }
+
+ public static String parseTokenChecked(String str, int ichMax, int[] next) {
+ int ich = next[0];
+ while (ich < ichMax && isWhiteSpace(str, ich))
+ ++ich;
+ int ichNonWhite = ich;
+ while (ich < ichMax && !isWhiteSpace(str, ich))
+ ++ich;
+ next[0] = ich;
+ return (ichNonWhite == ich ? null : str.substring(ichNonWhite, ich));
+ }
+
+ public static String parseTrimmedChecked(String str, int ich, int ichMax) {
+ while (ich < ichMax && isWhiteSpace(str, ich))
+ ++ich;
+ int ichLast = ichMax - 1;
+ while (ichLast >= ich && isWhiteSpace(str, ichLast))
+ --ichLast;
+ return (ichLast < ich ? "" : str.substring(ich, ichLast + 1));
+ }
+
+ public static double dVal(String s) throws NumberFormatException {
+ /**
+ * @j2sNative
+ *
+ * if(s==null)
+ * throw new NumberFormatException("null");
+ * var d=parseFloat(s);
+ * if(isNaN(d))
+ * throw new NumberFormatException("Not a Number : "+s);
+ * return d
+ *
+ */
+ {
+ return Double.valueOf(s).doubleValue();
+ }
+ }
+
+ public static float fVal(String s) throws NumberFormatException {
+ /**
+ * @j2sNative
+ *
+ * return this.dVal(s);
+ */
+ {
+ return Float.parseFloat(s);
+ }
+ }
+
+ public static int parseIntRange(String str, int ichMax, int[] next) {
+ int cch = str.length();
+ if (ichMax > cch)
+ ichMax = cch;
+ return (next[0] < 0 || next[0] >= ichMax ? Integer.MIN_VALUE : parseIntChecked(str, ichMax, next));
+ }
+
+ /**
+ * parses a string array for floats. Returns NaN for nonfloats.
+ *
+ * @param tokens the strings to parse
+ * @param data the array to fill
+ */
+ public static void parseFloatArrayData(String[] tokens, float[] data) {
+ parseFloatArrayDataN(tokens, data, data.length);
+ }
+
+ /**
+ * parses a string array for floats. Returns NaN for nonfloats or missing data.
+ *
+ * @param tokens the strings to parse
+ * @param data the array to fill
+ * @param nData the number of elements
+ */
+ public static void parseFloatArrayDataN(String[] tokens, float[] data, int nData) {
+ for (int i = nData; --i >= 0;)
+ data[i] = (i >= tokens.length ? Float.NaN : parseFloat(tokens[i]));
+ }
+
+ /**
+ *
+ * proper splitting, even for Java 1.3 -- if the text ends in the run,
+ * no new line is appended.
+ *
+ * @param text
+ * @param run
+ * @return String array
+ */
+ public static String[] split(String text, String run) {
+ if (text.length() == 0)
+ return new String[0];
+ int n = 1;
+ int i = text.indexOf(run);
+ String[] lines;
+ int runLen = run.length();
+ if (i < 0 || runLen == 0) {
+ lines = new String[1];
+ lines[0] = text;
+ return lines;
+ }
+ int len = text.length() - runLen;
+ for (; i >= 0 && i < len; n++)
+ i = text.indexOf(run, i + runLen);
+ lines = new String[n];
+ i = 0;
+ int ipt = 0;
+ int pt = 0;
+ for (; (ipt = text.indexOf(run, i)) >= 0 && pt + 1 < n;) {
+ lines[pt++] = text.substring(i, ipt);
+ i = ipt + runLen;
+ }
+ if (text.indexOf(run, len) != len)
+ len += runLen;
+ lines[pt] = text.substring(i, len);
+ return lines;
+ }
+
+ public final static float FLOAT_MIN_SAFE = 2E-45f;
+ // Float.MIN_VALUE (1.45E-45) is not reliable with JavaScript because of the float/double difference there
+
+ /// general static string-parsing class ///
+
+ // next[0] tracks the pointer within the string so these can all be static.
+ // but the methods parseFloat, parseInt, parseToken, parseTrimmed, and getTokens do not require this.
+
+// public static String concatTokens(String[] tokens, int iFirst, int iEnd) {
+// String str = "";
+// String sep = "";
+// for (int i = iFirst; i < iEnd; i++) {
+// if (i < tokens.length) {
+// str += sep + tokens[i];
+// sep = " ";
+// }
+// }
+// return str;
+// }
+
+ public static String getQuotedStringAt(String line, int ipt0) {
+ int[] next = new int[] { ipt0 };
+ return getQuotedStringNext(line, next);
+ }
+
+ /**
+ *
+ * @param line
+ * @param next passes [current pointer]
+ * @return quoted string -- does NOT unescape characters
+ */
+ public static String getQuotedStringNext(String line, int[] next) {
+ int i = next[0];
+ if (i < 0 || (i = line.indexOf("\"", i)) < 0)
+ return "";
+ int pt = i + 1;
+ int len = line.length();
+ while (++i < len && line.charAt(i) != '"')
+ if (line.charAt(i) == '\\')
+ i++;
+ next[0] = i + 1;
+ return line.substring(pt, i);
+ }
+
+ /**
+ * CSV format -- escaped quote is "" WITHIN "..."
+ *
+ *
+ * @param line
+ * @param next int[2] filled with [ptrQuote1, ptrAfterQuote2]
+ * next[1] will be -1 if unmatched quotes are found (continuation on next line)
+ * @return unescaped string or null
+ */
+ public static String getCSVString(String line, int[] next) {
+ int i = next[1];
+ if (i < 0 || (i = line.indexOf("\"", i)) < 0)
+ return null;
+ int pt = next[0] = i;
+ int len = line.length();
+ boolean escaped = false;
+ boolean haveEscape = false;
+ while (++i < len
+ && (line.charAt(i) != '"' || (escaped = (i + 1 < len && line.charAt(i + 1) == '"'))))
+ if (escaped) {
+ escaped = false;
+ haveEscape = true;
+ i++;
+ }
+ if (i >= len) {
+ next[1] = -1;
+ return null; // unmatched
+ }
+ next[1] = i + 1;
+ String s = line.substring(pt + 1, i);
+ return (haveEscape ? rep(rep(s, "\"\"", "\0"), "\0","\"") : s);
+ }
+
+ public static boolean isOneOf(String key, String semiList) {
+ if (semiList.length() == 0)
+ return false;
+ if (semiList.charAt(0) != ';')
+ semiList = ";" + semiList + ";";
+ return key.indexOf(";") < 0 && semiList.indexOf(';' + key + ';') >= 0;
+ }
+
+ public static String getQuotedAttribute(String info, String name) {
+ int i = info.indexOf(name + "=");
+ return (i < 0 ? null : getQuotedStringAt(info, i));
+ }
+
+ public static float approx(float f, float n) {
+ return Math.round (f * n) / n;
+ }
+
+ /**
+ * Does a clean ITERATIVE replace of strFrom in str with strTo.
+ * Thus, rep("Testttt", "tt","t") becomes "Test".
+ *
+ * @param str
+ * @param strFrom
+ * @param strTo
+ * @return replaced string
+ */
+ public static String rep(String str, String strFrom, String strTo) {
+ if (str == null || strFrom.length() == 0 || str.indexOf(strFrom) < 0)
+ return str;
+ boolean isOnce = (strTo.indexOf(strFrom) >= 0);
+ do {
+ str = str.replace(strFrom, strTo);
+ } while (!isOnce && str.indexOf(strFrom) >= 0);
+ return str;
+ }
+
+ public static String formatF(float value, int width, int precision,
+ boolean alignLeft, boolean zeroPad) {
+ return formatS(DF.formatDecimal(value, precision), width, 0, alignLeft, zeroPad);
+ }
+
+ /**
+ *
+ * @param value
+ * @param width
+ * @param precision
+ * @param alignLeft
+ * @param zeroPad
+ * @param allowOverflow IGNORED
+ * @return formatted string
+ */
+ public static String formatD(double value, int width, int precision,
+ boolean alignLeft, boolean zeroPad, boolean allowOverflow) {
+ return formatS(DF.formatDecimal((float)value, -1 - precision), width, 0, alignLeft, zeroPad);
+ }
+
+ /**
+ *
+ * @param value
+ * @param width number of columns
+ * @param precision precision > 0 ==> precision = number of characters max from left
+ * precision < 0 ==> -1 - precision = number of char. max from right
+ * @param alignLeft
+ * @param zeroPad generally for numbers turned strings
+ * @return formatted string
+ */
+ public static String formatS(String value, int width, int precision,
+ boolean alignLeft, boolean zeroPad) {
+ if (value == null)
+ return "";
+ int len = value.length();
+ if (precision != Integer.MAX_VALUE && precision > 0
+ && precision < len)
+ value = value.substring(0, precision);
+ else if (precision < 0 && len + precision >= 0)
+ value = value.substring(len + precision + 1);
+
+ int padLength = width - value.length();
+ if (padLength <= 0)
+ return value;
+ boolean isNeg = (zeroPad && !alignLeft && value.charAt(0) == '-');
+ char padChar = (zeroPad ? '0' : ' ');
+ char padChar0 = (isNeg ? '-' : padChar);
+
+ SB sb = new SB();
+ if (alignLeft)
+ sb.append(value);
+ sb.appendC(padChar0);
+ for (int i = padLength; --i > 0;)
+ // this is correct, not >= 0
+ sb.appendC(padChar);
+ if (!alignLeft)
+ sb.append(isNeg ? padChar + value.substring(1) : value);
+ return sb.toString();
+ }
+
+ /**
+ * Does a clean replace of any of the characters in str with chrTo
+ * If strTo contains strFrom, then only a single pass is done.
+ * Otherwise, multiple passes are made until no more replacements can be made.
+ *
+ * @param str
+ * @param strFrom
+ * @param chTo
+ * @return replaced string
+ */
+ public static String replaceWithCharacter(String str, String strFrom,
+ char chTo) {
+ if (str == null)
+ return null;
+ for (int i = strFrom.length(); --i >= 0;)
+ str = str.replace(strFrom.charAt(i), chTo);
+ return str;
+ }
+
+ /**
+ * Does a clean replace of any of the characters in str with strTo
+ * If strTo contains strFrom, then only a single pass is done.
+ * Otherwise, multiple passes are made until no more replacements can be made.
+ *
+ * @param str
+ * @param strFrom
+ * @param strTo
+ * @return replaced string
+ */
+ public static String replaceAllCharacters(String str, String strFrom,
+ String strTo) {
+ for (int i = strFrom.length(); --i >= 0;) {
+ String chFrom = strFrom.substring(i, i + 1);
+ str = rep(str, chFrom, strTo);
+ }
+ return str;
+ }
+
+ public static String trim(String str, String chars) {
+ if (str == null || str.length() == 0)
+ return str;
+ if (chars.length() == 0)
+ return str.trim();
+ int len = str.length();
+ int k = 0;
+ while (k < len && chars.indexOf(str.charAt(k)) >= 0)
+ k++;
+ int m = str.length() - 1;
+ while (m > k && chars.indexOf(str.charAt(m)) >= 0)
+ m--;
+ return str.substring(k, m + 1);
+ }
+
+ public static String trimQuotes(String value) {
+ return (value != null && value.length() > 1 && value.startsWith("\"")
+ && value.endsWith("\"") ? value.substring(1, value.length() - 1)
+ : value);
+ }
+
+ public static boolean isNonStringPrimitive(Object info) {
+ // note that we don't use Double, Float, or Integer here
+ // because in JavaScript those would be false for unwrapped primitives
+ // coming from equivalent of Array.get()
+ // Strings will need their own escaped processing
+
+ return info instanceof Number || info instanceof Boolean;
+ }
+
+ private static Object arrayGet(Object info, int i) {
+ /**
+ *
+ * Note that info will be a primitive in JavaScript
+ * but a wrapped primitive in Java.
+ *
+ * @j2sNative
+ *
+ * return info[i];
+ */
+ {
+ return Array.get(info, i);
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ public static String toJSON(String infoType, Object info) {
+ if (info == null)
+ return packageJSON(infoType, null);
+ if (isNonStringPrimitive(info))
+ return packageJSON(infoType, info.toString());
+ String s = null;
+ SB sb = null;
+ while (true) {
+ if (info instanceof String) {
+ s = (String) info;
+ /**
+ * @j2sNative
+ *
+ * if (typeof s == "undefined") s = "null"
+ *
+ */
+ {}
+
+ if (s.indexOf("{\"") != 0) {
+ //don't doubly fix JSON strings when retrieving status
+ // what about \1 \2 \3 etc.?
+ s = esc(s);
+ }
+ break;
+ }
+ if (info instanceof JSONEncodable) {
+ // includes javajs.util.BS, org.jmol.script.SV
+ if ((s = ((JSONEncodable) info).toJSON()) == null)
+ s = "null"; // perhaps a list has a null value (group3List, for example)
+ break;
+ }
+ sb = new SB();
+ if (info instanceof Map) {
+ sb.append("{ ");
+ String sep = "";
+ for (String key : ((Map<String, ?>) info).keySet()) {
+ sb.append(sep).append(
+ packageJSON(key, toJSON(null, ((Map<?, ?>) info).get(key))));
+ sep = ",";
+ }
+ sb.append(" }");
+ break;
+ }
+ if (info instanceof Lst) {
+ sb.append("[ ");
+ int n = ((Lst<?>) info).size();
+ for (int i = 0; i < n; i++) {
+ if (i > 0)
+ sb.appendC(',');
+ sb.append(toJSON(null, ((Lst<?>) info).get(i)));
+ }
+ sb.append(" ]");
+ break;
+ }
+ if (info instanceof M34) {
+ // M4 extends M3
+ int len = (info instanceof M4 ? 4 : 3);
+ float[] x = new float[len];
+ M34 m = (M34) info;
+ sb.appendC('[');
+ for (int i = 0; i < len; i++) {
+ if (i > 0)
+ sb.appendC(',');
+ m.getRow(i, x);
+ sb.append(toJSON(null, x));
+ }
+ sb.appendC(']');
+ break;
+ }
+ s = nonArrayString(info);
+ if (s == null) {
+ sb.append("[");
+ int n = AU.getLength(info);
+ for (int i = 0; i < n; i++) {
+ if (i > 0)
+ sb.appendC(',');
+ sb.append(toJSON(null, arrayGet(info, i)));
+ }
+ sb.append("]");
+ break;
+ }
+ info = info.toString();
+ }
+ return packageJSON(infoType, (s == null ? sb.toString() : s));
+ }
+
+ /**
+ * Checks to see if an object is an array (including typed arrays), and if it is, returns null;
+ * otherwise it returns the string equivalent of that object.
+ *
+ * @param x
+ * @return String or null
+ */
+ public static String nonArrayString(Object x) {
+ /**
+ * @j2sNative
+ *
+ * return (x.constructor == Array || x.__BYTESIZE ? null : x.toString());
+ *
+ */
+ {
+ try {
+ Array.getLength(x);
+ return null;
+ } catch (Exception e) {
+ return x.toString();
+ }
+ }
+ }
+
+ public static String byteArrayToJSON(byte[] data) {
+ SB sb = new SB();
+ sb.append("[");
+ int n = data.length;
+ for (int i = 0; i < n; i++) {
+ if (i > 0)
+ sb.appendC(',');
+ sb.appendI(data[i] & 0xFF);
+ }
+ sb.append("]");
+ return sb.toString();
+ }
+
+ public static String packageJSON(String infoType, String info) {
+ return (infoType == null ? info : "\"" + infoType + "\": " + info);
+ }
+
+ public static String escapeUrl(String url) {
+ url = rep(url, "\n", "");
+ url = rep(url, "%", "%25");
+ url = rep(url, "#", "%23");
+ url = rep(url, "[", "%5B");
+ url = rep(url, "\\", "%5C");
+ url = rep(url, "]", "%5D");
+ url = rep(url, " ", "%20");
+ return url;
+ }
+
+ private final static String escapable = "\\\\\tt\rr\nn\"\"";
+
+ public static String esc(String str) {
+ if (str == null || str.length() == 0)
+ return "\"\"";
+ boolean haveEscape = false;
+ int i = 0;
+ for (; i < escapable.length(); i += 2)
+ if (str.indexOf(escapable.charAt(i)) >= 0) {
+ haveEscape = true;
+ break;
+ }
+ if (haveEscape)
+ while (i < escapable.length()) {
+ int pt = -1;
+ char ch = escapable.charAt(i++);
+ char ch2 = escapable.charAt(i++);
+ SB sb = new SB();
+ int pt0 = 0;
+ while ((pt = str.indexOf(ch, pt + 1)) >= 0) {
+ sb.append(str.substring(pt0, pt)).appendC('\\').appendC(ch2);
+ pt0 = pt + 1;
+ }
+ sb.append(str.substring(pt0, str.length()));
+ str = sb.toString();
+ }
+ return "\"" + escUnicode(str) + "\"";
+ }
+
+ public static String escUnicode(String str) {
+ for (int i = str.length(); --i >= 0;)
+ if (str.charAt(i) > 0x7F) {
+ String s = "0000" + Integer.toHexString(str.charAt(i));
+ str = str.substring(0, i) + "\\u" + s.substring(s.length() - 4)
+ + str.substring(i + 1);
+ }
+ return str;
+ }
+
+ /**
+ * ensures that a float turned to string has a decimal point
+ *
+ * @param f
+ * @return string version of float
+ */
+ public static String escF(float f) {
+ String sf = "" + f;
+ /**
+ * @j2sNative
+ *
+ * if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0)
+ * sf += ".0";
+ */
+ {
+ }
+ return sf;
+ }
+ public static String join(String[] s, char c, int i0) {
+ if (s.length < i0)
+ return null;
+ SB sb = new SB();
+ sb.append(s[i0++]);
+ for (int i = i0; i < s.length; i++)
+ sb.appendC(c).append(s[i]);
+ return sb.toString();
+ }
+
+ /**
+ * a LIKE "x" a is a string and equals x
+ *
+ * a LIKE "*x" a is a string and ends with x
+ *
+ * a LIKE "x*" a is a string and starts with x
+ *
+ * a LIKE "*x*" a is a string and contains x
+ *
+ * @param a
+ * @param b
+ * @return a LIKE b
+ */
+ public static boolean isLike(String a, String b) {
+ boolean areEqual = a.equals(b);
+ if (areEqual)
+ return true;
+ boolean isStart = b.startsWith("*");
+ boolean isEnd = b.endsWith("*");
+ return (!isStart && !isEnd) ? areEqual
+ : isStart && isEnd ? b.length() == 1 || a.contains(b.substring(1, b.length() - 1))
+ : isStart ? a.endsWith(b.substring(1))
+ : a.startsWith(b.substring(0, b.length() - 1));
+ }
+
+ public static Object getMapValueNoCase(Map<String, ?> h, String key) {
+ if ("this".equals(key))
+ return h;
+ Object val = h.get(key);
+ if (val == null)
+ for (Entry<String, ?> e : h.entrySet())
+ if (e.getKey().equalsIgnoreCase(key))
+ return e.getValue();
+ return val;
+ }
+
+ public static String clean(String s) {
+ return rep(replaceAllCharacters(s, " \t\n\r", " "), " ", " ").trim();
+ }
+
+ /**
+ *
+ * fdup duplicates p or q formats for formatCheck
+ * and the format() function.
+ *
+ * @param f
+ * @param pt
+ * @param n
+ * @return %3.5q%3.5q%3.5q%3.5q or %3.5p%3.5p%3.5p
+ */
+ public static String fdup(String f, int pt, int n) {
+ char ch;
+ int count = 0;
+ for (int i = pt; --i >= 1; ) {
+ if (isDigit(ch = f.charAt(i)))
+ continue;
+ switch (ch) {
+ case '.':
+ if (count++ != 0)
+ return f;
+ continue;
+ case '-':
+ if (i != 1 && f.charAt(i - 1) != '.')
+ return f;
+ continue;
+ default:
+ return f;
+ }
+ }
+ String s = f.substring(0, pt + 1);
+ SB sb = new SB();
+ for (int i = 0; i < n; i++)
+ sb.append(s);
+ sb.append(f.substring(pt + 1));
+ return sb.toString();
+ }
+
+ /**
+ * generic string formatter based on formatLabel in Atom
+ *
+ *
+ * @param strFormat .... %width.precisionKEY....
+ * @param key any string to match
+ * @param strT replacement string or null
+ * @param floatT replacement float or Float.NaN
+ * @param doubleT replacement double or Double.NaN -- for exponential
+ * @param doOne mimic sprintf
+ * @return formatted string
+ */
+
+ private static String formatString(String strFormat, String key, String strT,
+ float floatT, double doubleT, boolean doOne) {
+ if (strFormat == null)
+ return null;
+ if ("".equals(strFormat))
+ return "";
+ int len = key.length();
+ if (strFormat.indexOf("%") < 0 || len == 0 || strFormat.indexOf(key) < 0)
+ return strFormat;
+
+ String strLabel = "";
+ int ich, ichPercent, ichKey;
+ for (ich = 0; (ichPercent = strFormat.indexOf('%', ich)) >= 0
+ && (ichKey = strFormat.indexOf(key, ichPercent + 1)) >= 0;) {
+ if (ich != ichPercent)
+ strLabel += strFormat.substring(ich, ichPercent);
+ ich = ichPercent + 1;
+ if (ichKey > ichPercent + 6) {
+ strLabel += '%';
+ continue;//%12.10x
+ }
+ try {
+ boolean alignLeft = false;
+ if (strFormat.charAt(ich) == '-') {
+ alignLeft = true;
+ ++ich;
+ }
+ boolean zeroPad = false;
+ if (strFormat.charAt(ich) == '0') {
+ zeroPad = true;
+ ++ich;
+ }
+ char ch;
+ int width = 0;
+ while ((ch = strFormat.charAt(ich)) >= '0' && (ch <= '9')) {
+ width = (10 * width) + (ch - '0');
+ ++ich;
+ }
+ int precision = Integer.MAX_VALUE;
+ boolean isExponential = false;
+ if (strFormat.charAt(ich) == '.') {
+ ++ich;
+ if ((ch = strFormat.charAt(ich)) == '-') {
+ isExponential = (strT == null);
+ ++ich;
+ }
+ if ((ch = strFormat.charAt(ich)) >= '0' && ch <= '9') {
+ precision = ch - '0';
+ ++ich;
+ }
+ if (isExponential)
+ precision = -precision;
+ }
+ String st = strFormat.substring(ich, ich + len);
+ if (!st.equals(key)) {
+ ich = ichPercent + 1;
+ strLabel += '%';
+ continue;
+ }
+ ich += len;
+ if (!Float.isNaN(floatT)) // 'f'
+ strLabel += formatF(floatT, width, precision, alignLeft,
+ zeroPad);
+ else if (strT != null) // 'd' 'i' or 's'
+ strLabel += formatS(strT, width, precision, alignLeft,
+ zeroPad);
+ else if (!Double.isNaN(doubleT)) // 'e'
+ strLabel += formatD(doubleT, width, precision - 1, alignLeft,
+ zeroPad, true);
+ if (doOne)
+ break;
+ } catch (IndexOutOfBoundsException ioobe) {
+ ich = ichPercent;
+ break;
+ }
+ }
+ strLabel += strFormat.substring(ich);
+ //if (strLabel.length() == 0)
+ //return null;
+ return strLabel;
+ }
+
+ public static String formatStringS(String strFormat, String key, String strT) {
+ return formatString(strFormat, key, strT, Float.NaN, Double.NaN, false);
+ }
+
+ public static String formatStringF(String strFormat, String key, float floatT) {
+ return formatString(strFormat, key, null, floatT, Double.NaN, false);
+ }
+
+ public static String formatStringI(String strFormat, String key, int intT) {
+ return formatString(strFormat, key, "" + intT, Float.NaN, Double.NaN, false);
+ }
+
+ /**
+ * sprintf emulation uses (almost) c++ standard string formats
+ *
+ * 's' string 'i' or 'd' integer, 'e' double, 'f' float, 'p' point3f 'q'
+ * quaternion/plane/axisangle with added "i" (equal to the insipid "d" --
+ * digits?)
+ *
+ * @param strFormat
+ * @param list
+ * a listing of what sort of data will be found in Object[] values, in
+ * order: s string, f float, i integer, d double, p point3f, q
+ * quaternion/point4f, S String[], F float[], I int[], and D double[]
+ * @param values
+ * Object[] containing above types
+ * @return formatted string
+ */
+ public static String sprintf(String strFormat, String list, Object[] values) {
+ if (values == null)
+ return strFormat;
+ int n = list.length();
+ if (n == values.length)
+ try {
+ for (int o = 0; o < n; o++) {
+ if (values[o] == null)
+ continue;
+ switch (list.charAt(o)) {
+ case 's':
+ strFormat = formatString(strFormat, "s", (String) values[o],
+ Float.NaN, Double.NaN, true);
+ break;
+ case 'f':
+ strFormat = formatString(strFormat, "f", null, ((Float) values[o])
+ .floatValue(), Double.NaN, true);
+ break;
+ case 'i':
+ strFormat = formatString(strFormat, "d", "" + values[o], Float.NaN,
+ Double.NaN, true);
+ strFormat = formatString(strFormat, "i", "" + values[o], Float.NaN,
+ Double.NaN, true);
+ break;
+ case 'd':
+ strFormat = formatString(strFormat, "e", null, Float.NaN,
+ ((Double) values[o]).doubleValue(), true);
+ break;
+ case 'p':
+ T3 pVal = (T3) values[o];
+ strFormat = formatString(strFormat, "p", null, pVal.x, Double.NaN,
+ true);
+ strFormat = formatString(strFormat, "p", null, pVal.y, Double.NaN,
+ true);
+ strFormat = formatString(strFormat, "p", null, pVal.z, Double.NaN,
+ true);
+ break;
+ case 'q':
+ T4 qVal = (T4) values[o];
+ strFormat = formatString(strFormat, "q", null, qVal.x, Double.NaN,
+ true);
+ strFormat = formatString(strFormat, "q", null, qVal.y, Double.NaN,
+ true);
+ strFormat = formatString(strFormat, "q", null, qVal.z, Double.NaN,
+ true);
+ strFormat = formatString(strFormat, "q", null, qVal.w, Double.NaN,
+ true);
+ break;
+ case 'S':
+ String[] sVal = (String[]) values[o];
+ for (int i = 0; i < sVal.length; i++)
+ strFormat = formatString(strFormat, "s", sVal[i], Float.NaN,
+ Double.NaN, true);
+ break;
+ case 'F':
+ float[] fVal = (float[]) values[o];
+ for (int i = 0; i < fVal.length; i++)
+ strFormat = formatString(strFormat, "f", null, fVal[i],
+ Double.NaN, true);
+ break;
+ case 'I':
+ int[] iVal = (int[]) values[o];
+ for (int i = 0; i < iVal.length; i++)
+ strFormat = formatString(strFormat, "d", "" + iVal[i], Float.NaN,
+ Double.NaN, true);
+ for (int i = 0; i < iVal.length; i++)
+ strFormat = formatString(strFormat, "i", "" + iVal[i], Float.NaN,
+ Double.NaN, true);
+ break;
+ case 'D':
+ double[] dVal = (double[]) values[o];
+ for (int i = 0; i < dVal.length; i++)
+ strFormat = formatString(strFormat, "e", null, Float.NaN,
+ dVal[i], true);
+ }
+
+ }
+ return rep(strFormat, "%%", "%");
+ } catch (Exception e) {
+ //
+ }
+ System.out.println("TextFormat.sprintf error " + list + " " + strFormat);
+ return rep(strFormat, "%", "?");
+ }
+
+ /**
+ *
+ * formatCheck checks p and q formats and duplicates if necessary
+ * "%10.5p xxxx" ==> "%10.5p%10.5p%10.5p xxxx"
+ *
+ * @param strFormat
+ * @return f or dupicated format
+ */
+ public static String formatCheck(String strFormat) {
+ if (strFormat == null || strFormat.indexOf('p') < 0 && strFormat.indexOf('q') < 0)
+ return strFormat;
+ strFormat = rep(strFormat, "%%", "\1");
+ strFormat = rep(strFormat, "%p", "%6.2p");
+ strFormat = rep(strFormat, "%q", "%6.2q");
+ String[] format = split(strFormat, "%");
+ SB sb = new SB();
+ sb.append(format[0]);
+ for (int i = 1; i < format.length; i++) {
+ String f = "%" + format[i];
+ int pt;
+ if (f.length() >= 3) {
+ if ((pt = f.indexOf('p')) >= 0)
+ f = fdup(f, pt, 3);
+ if ((pt = f.indexOf('q')) >= 0)
+ f = fdup(f, pt, 4);
+ }
+ sb.append(f);
+ }
+ return sb.toString().replace('\1', '%');
+ }
+
+ public static void leftJustify(SB s, String s1, String s2) {
+ s.append(s2);
+ int n = s1.length() - s2.length();
+ if (n > 0)
+ s.append(s1.substring(0, n));
+ }
+
+ public static void rightJustify(SB s, String s1, String s2) {
+ int n = s1.length() - s2.length();
+ if (n > 0)
+ s.append(s1.substring(0, n));
+ s.append(s2);
+ }
+
+ public static String safeTruncate(float f, int n) {
+ if (f > -0.001 && f < 0.001)
+ f = 0;
+ return (f + " ").substring(0,n);
+ }
+
+ public static boolean isWild(String s) {
+ return s != null && (s.indexOf("*") >= 0 || s.indexOf("?") >= 0);
+ }
+
+ /**
+ * A general non-regex (for performance) text matcher that utilizes ? and *.
+ *
+ * ??? means "at most three" characters if at beginning or end;
+ * "exactly three" otherwise
+ * \1 in search is a stand-in for actual ?
+ *
+ * @param search
+ * the string to search
+ * @param match
+ * the match string
+ * @param checkStar
+ * @param allowInitialStar
+ * @return true if found
+ */
+ public static boolean isMatch(String search, String match, boolean checkStar,
+ boolean allowInitialStar) {
+ // search == match --> true
+ if (search.equals(match))
+ return true;
+ int mLen = match.length();
+ // match == "" --> false
+ if (mLen == 0)
+ return false;
+ boolean isStar0 = (checkStar && allowInitialStar ? match.charAt(0) == '*'
+ : false);
+ // match == "*" --> true
+ if (mLen == 1 && isStar0)
+ return true;
+ boolean isStar1 = (checkStar && match.endsWith("*"));
+ boolean haveQ = (match.indexOf('?') >= 0);
+ // match == "**" --> true
+ // match == "*xxx*" --> search contains "xxx"
+ // match == "*xxx" --> search ends with "xxx"
+ // match == "xxx*" --> search starts with "xxx"
+ if (!haveQ) {
+ if (isStar0)
+ return (isStar1 ? (mLen < 3 || search.indexOf(match.substring(1,
+ mLen - 1)) >= 0) : search.endsWith(match.substring(1)));
+ else if (isStar1)
+ return search.startsWith(match.substring(0, mLen - 1));
+ }
+ int sLen = search.length();
+ // pad match with "?" -- same as *
+ String qqqq = "????";
+ int nq = 4;
+ while (nq < sLen) {
+ qqqq += qqqq;
+ nq += 4;
+ }
+ if (checkStar) {
+ if (isStar0) {
+ match = qqqq + match.substring(1);
+ mLen += nq - 1;
+ }
+ if (isStar1) {
+ match = match.substring(0, mLen - 1) + qqqq;
+ mLen += nq - 1;
+ }
+ }
+ // length of match < length of search --> false
+ if (mLen < sLen)
+ return false;
+
+ // -- each ? matches ONE character if not at end
+ // -- extra ? at end ignored
+
+ // (allowInitialStar == true)
+ // -- extra ? at beginning reduced to match length
+
+ int ich = 0;
+ while (mLen > sLen) {
+ if (allowInitialStar && match.charAt(ich) == '?') {
+ ++ich;
+ } else if (match.charAt(ich + mLen - 1) != '?') {
+ return false;
+ }
+ --mLen;
+ }
+
+ // both are effectively same length now.
+ // \1 is stand-in for "?"
+
+ for (int i = sLen; --i >= 0;) {
+ char chm = match.charAt(ich + i);
+ if (chm == '?')
+ continue;
+ char chs = search.charAt(i);
+ if (chm != chs && (chm != '\1' || chs != '?'))
+ return false;
+ }
+ return true;
+ }
+
+ public static String replaceQuotedStrings(String s, Lst<String> list,
+ Lst<String> newList) {
+ int n = list.size();
+ for (int i = 0; i < n; i++) {
+ String name = list.get(i);
+ String newName = newList.get(i);
+ if (!newName.equals(name))
+ s = rep(s, "\"" + name + "\"", "\"" + newName
+ + "\"");
+ }
+ return s;
+ }
+
+ public static String replaceStrings(String s, Lst<String> list,
+ Lst<String> newList) {
+ int n = list.size();
+ for (int i = 0; i < n; i++) {
+ String name = list.get(i);
+ String newName = newList.get(i);
+ if (!newName.equals(name))
+ s = rep(s, name, newName);
+ }
+ return s;
+ }
+
+ public static boolean isDigit(char ch) {
+ // just way simpler code than Character.isDigit(ch);
+ int c = ch;
+ return (48 <= c && c <= 57);
+ }
+
+ public static boolean isUpperCase(char ch) {
+ int c = ch;
+ return (65 <= c && c <= 90);
+ }
+
+ public static boolean isLowerCase(char ch) {
+ int c = ch;
+ return (97 <= c && c <= 122);
+ }
+
+ public static boolean isLetter(char ch) {
+ // just way simpler code than Character.isLetter(ch);
+ int c = ch;
+ return (65 <= c && c <= 90 || 97 <= c && c <= 122);
+ }
+
+ public static boolean isLetterOrDigit(char ch) {
+ // just way simpler code than Character.isLetterOrDigit(ch);
+ int c = ch;
+ return (65 <= c && c <= 90 || 97 <= c && c <= 122 || 48 <= c && c <= 57);
+ }
+
+ public static boolean isWhitespace(char ch) {
+ int c = ch;
+ return (c >= 0x1c && c <= 0x20 || c >= 0x9 && c <= 0xd);
+ }
+
+ public static final float FRACTIONAL_PRECISION = 100000f;
+ public static final float CARTESIAN_PRECISION = 10000f;
+
+ public static void fixPtFloats(T3 pt, float f) {
+ //this will equate float and double as long as -256 <= x <= 256
+ pt.x = Math.round(pt.x * f) / f;
+ pt.y = Math.round(pt.y * f) / f;
+ pt.z = Math.round(pt.z * f) / f;
+ }
+
+ public static double fixDouble(double d, double f) {
+ return Math.round(d * f) / f;
+ }
+
+ /**
+ * parse a float or "float/float"
+ * @param s
+ * @return a/b
+ */
+ public static float parseFloatFraction(String s) {
+ int pt = s.indexOf("/");
+ return (pt < 0 ? parseFloat(s) : parseFloat(s.substring(0, pt))
+ / parseFloat(s.substring(pt + 1)));
+ }
+
+//static {
+//
+// double d = 790.8999998888;
+// float x = 790.8999998888f;
+// for (int i = 0; i < 50; i++) {
+// System.out.println(x + " " + d);
+// System.out.println(Math.round(x * 100000) / 100000f);
+// System.out.println(Math.round(d * 100000) / 100000.);
+// System.out.println(Math.round(x * 10000) / 10000f);
+// System.out.println(Math.round(d * 10000) / 10000.);
+// x+=1;
+// d+=1;
+// }
+// System.out.println(100.123456789f);
+//}
+
+// static {
+// long t;
+// char c = '0';
+// t = System.currentTimeMillis();
+// for (int i = 0; i < 10000000; i++) {
+// boolean b = PT.isUpperCase(c);
+// }
+// System.out.println(System.currentTimeMillis() - t);
+//
+// t = System.currentTimeMillis();
+// for (int i = 0; i < 10000000; i++) {
+// boolean b = Character.isUpperCase(c);
+// }
+// System.out.println(System.currentTimeMillis() - t);
+//
+// t = System.currentTimeMillis();
+// for (int i = 0; i < 10000000; i++) {
+// boolean b = PT.isUpperCase(c);
+// }
+// System.out.println(System.currentTimeMillis() - t);
+//
+// System.out.println("PT test");
+// }
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-04-05 09:07:28 -0500 (Thu, 05 Apr 2007) $
+ * $Revision: 7326 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.util;
+
+/*
+ * Standard UNIT quaternion math -- for rotation.
+ *
+ * All rotations can be represented as two identical quaternions.
+ * This is because any rotation can be considered from either end of the
+ * rotational axis -- either as a + rotation or a - rotation. This code
+ * is designed to always maintain the quaternion with a rotation in the
+ * [0, PI) range.
+ *
+ * This ensures that the reported theta is always positive, and the normal
+ * reported is always associated with a positive theta.
+ *
+ * @author Bob Hanson, hansonr@stolaf.edu 6/2008
+ *
+ */
+
+public class Quat {
+ public float q0, q1, q2, q3;
+ private M3 mat;
+
+ private final static P4 qZero = new P4();
+ private static final double RAD_PER_DEG = Math.PI / 180;
+
+ public Quat() {
+ q0 = 1;
+ }
+
+ public static Quat newQ(Quat q) {
+ Quat q1 = new Quat();
+ q1.set(q);
+ return q1;
+ }
+
+ public static Quat newVA(T3 v, float theta) {
+ Quat q = new Quat();
+ q.setTA(v, theta);
+ return q;
+ }
+
+ public static Quat newM(M3 mat) {
+ Quat q = new Quat();
+ q.setM(M3.newM3(mat));
+ return q;
+ }
+
+ public static Quat newAA(A4 a) {
+ Quat q = new Quat();
+ q.setAA(a);
+ return q;
+ }
+
+ public static Quat newP4(P4 pt) {
+ Quat q = new Quat();
+ q.setP4(pt);
+ return q;
+ }
+
+ /**
+ * Note that q0 is the last parameter here
+ *
+ * @param q1
+ * @param q2
+ * @param q3
+ * @param q0
+ * @return {q1 q2 q3 q0}
+ */
+ public static Quat new4(float q1, float q2, float q3, float q0) {
+ Quat q = new Quat();
+ if (q0 < -1) {
+ q.q0 = -1;
+ return q;
+ }
+ if (q0 > 1) {
+ q.q0 = 1;
+ return q;
+ }
+ q.q0 = q0;
+ q.q1 = q1;
+ q.q2 = q2;
+ q.q3 = q3;
+ return q;
+ }
+
+ public void set(Quat q) {
+ q0 = q.q0;
+ q1 = q.q1;
+ q2 = q.q2;
+ q3 = q.q3;
+ }
+
+ /**
+ * {x y z w} --> {q1 q2 q3 q0} and factored
+ *
+ * @param pt
+ */
+ private void setP4(P4 pt) {
+ float factor = (pt == null ? 0 : pt.distance4(qZero));
+ if (factor == 0) {
+ q0 = 1;
+ return;
+ }
+ q0 = pt.w / factor;
+ q1 = pt.x / factor;
+ q2 = pt.y / factor;
+ q3 = pt.z / factor;
+ }
+
+ /**
+ * q = (cos(theta/2), sin(theta/2) * n)
+ *
+ * @param pt
+ * @param theta
+ */
+ public void setTA(T3 pt, float theta) {
+ if (pt.x == 0 && pt.y == 0 && pt.z == 0) {
+ q0 = 1;
+ return;
+ }
+ double fact = (Math.sin(theta / 2 * RAD_PER_DEG) / Math.sqrt(pt.x
+ * pt.x + pt.y * pt.y + pt.z * pt.z));
+ q0 = (float) (Math.cos(theta / 2 * RAD_PER_DEG));
+ q1 = (float) (pt.x * fact);
+ q2 = (float) (pt.y * fact);
+ q3 = (float) (pt.z * fact);
+ }
+
+ public void setAA(A4 a) {
+ A4 aa = A4.newAA(a);
+ if (aa.angle == 0)
+ aa.y = 1;
+ setM(new M3().setAA(aa));
+ }
+
+ private void setM(M3 mat) {
+
+ /*
+ * Changed 7/16/2008 to double precision for 11.5.48.
+ *
+ * <quote>
+ *
+ * RayTrace Software Package, release 3.0. May 3, 2006.
+ *
+ * Mathematics Subpackage (VrMath)
+ *
+ * Author: Samuel R. Buss
+ *
+ * Software is "as-is" and carries no warranty. It may be used without
+ * restriction, but if you modify it, please change the filenames to
+ * prevent confusion between different versions. Please acknowledge
+ * all use of the software in any publications or products based on it.
+ *
+ * Bug reports: Sam Buss, sbuss@ucsd.edu.
+ * Web page: http://math.ucsd.edu/~sbuss/MathCG
+
+ // Use Shepperd's algorithm, which is stable, does not lose
+ // significant precision and uses only one sqrt.
+ // J. Guidance and Control, 1 (1978) 223-224.
+
+ * </quote>
+ *
+ * Except, that code has errors.
+ *
+ * CORRECTIONS (as noted below) of Quaternion.cpp. I have reported the bug.
+ *
+ * -- Bob Hanson
+ *
+ * theory:
+ * cos(theta/2)^2 = (cos(theta) + 1)/2
+ * and
+ * trace = (1-x^2)ct + (1-y^2)ct + (1-z^2)ct + 1 = 2cos(theta) + 1
+ * or
+ * cos(theta) = (trace - 1)/2
+ *
+ * so in general,
+ *
+ * w = cos(theta/2)
+ * = sqrt((cos(theta)+1)/2)
+ * = sqrt((trace-1)/4+1/2)
+ * = sqrt((trace+1)/4)
+ * = sqrt(trace+1)/2
+ *
+ * but there are precision issues, so we allow for other situations.
+ * note -- trace >= 0.5 when cos(theta) >= -0.25 (-104.48 <= theta <= 104.48).
+ * this code cleverly matches the precision in all four options.
+ *
+ */
+
+ this.mat = mat;
+
+ double trace = mat.m00 + mat.m11 + mat.m22;
+ double temp;
+ double w, x, y, z;
+ if (trace >= 0.5) {
+ w = Math.sqrt(1.0 + trace);
+ x = (mat.m21 - mat.m12) / w;
+ y = (mat.m02 - mat.m20) / w;
+ z = (mat.m10 - mat.m01) / w;
+ } else if ((temp = mat.m00 + mat.m00 - trace) >= 0.5) {
+ x = Math.sqrt(1.0 + temp);
+ w = (mat.m21 - mat.m12) / x;
+ y = (mat.m10 + mat.m01) / x;
+ z = (mat.m20 + mat.m02) / x;
+ } else if ((temp = mat.m11 + mat.m11 - trace) >= 0.5
+ || mat.m11 > mat.m22) {
+ y = Math.sqrt(1.0 + temp);
+ w = (mat.m02 - mat.m20) / y;
+ x = (mat.m10 + mat.m01) / y;
+ z = (mat.m21 + mat.m12) / y;
+ } else {
+ z = Math.sqrt(1.0 + mat.m22 + mat.m22 - trace);
+ w = (mat.m10 - mat.m01) / z;
+ x = (mat.m20 + mat.m02) / z; // was -
+ y = (mat.m21 + mat.m12) / z; // was -
+ }
+
+ q0 = (float) (w * 0.5);
+ q1 = (float) (x * 0.5);
+ q2 = (float) (y * 0.5);
+ q3 = (float) (z * 0.5);
+
+ /*
+ * Originally from http://www.gamedev.net/community/forums/topic.asp?topic_id=448380
+ * later algorithm was adapted from Visualizing Quaternions, by Andrew J. Hanson
+ * (Morgan Kaufmann, 2006), page 446
+ *
+ * HOWEVER, checking with AxisAngle4f and Quat4f equivalents, it was found that
+ * BOTH of these sources produce inverted quaternions. So here we do an inversion.
+ *
+ * This correction was made in 11.5.42 6/19/2008 -- Bob Hanson
+ *
+ * former algorithm used:
+ * /
+
+ double tr = mat.m00 + mat.m11 + mat.m22; //Matrix trace
+ double s;
+ double[] q = new double[4];
+ if (tr > 0) {
+ s = Math.sqrt(tr + 1);
+ q0 = (float) (0.5 * s);
+ s = 0.5 / s; // = 1/q0
+ q1 = (float) ((mat.m21 - mat.m12) * s);
+ q2 = (float) ((mat.m02 - mat.m20) * s);
+ q3 = (float) ((mat.m10 - mat.m01) * s);
+ } else {
+ float[][] m = new float[][] { new float[3], new float[3], new float[3] };
+ mat.getRow(0, m[0]);
+ mat.getRow(1, m[1]);
+ mat.getRow(2, m[2]);
+
+ //Find out the biggest element along the diagonal
+ float max = Math.max(mat.m11, mat.m00);
+ int i = (mat.m22 > max ? 2 : max == mat.m11 ? 1 : 0);
+ int j = (i + 1) % 3;
+ int k = (j + 1) % 3;
+ s = -Math.sqrt(1 + m[i][i] - m[j][j] - m[k][k]);
+ // 0 = 1 + (1-x^2)ct + x^2 -(1-y^2)ct - y^2 - (1-z^2)ct - z^2
+ // 0 = 1 - ct + (x^2 - y^2 - z^2) - (x^2 - y^2 - z^2)ct
+ // 0 = 1 - ct + 2x^2 - 1 - (2x^2)ct + ct
+ // 0 = 2x^2(1 - ct)
+ // theta = 0 (but then trace = 1 + 1 + 1 = 3)
+ // or x = 0.
+ q[i] = s * 0.5;
+ if (s != 0)
+ s = 0.5 / s; // = 1/q[i]
+ q[j] = (m[i][j] + m[j][i]) * s;
+ q[k] = (m[i][k] + m[k][i]) * s;
+ q0 = (float) ((m[k][j] - m[j][k]) * s);
+ q1 = (float) q[0]; // x
+ q2 = (float) q[1]; // y
+ q3 = (float) q[2]; // z
+ }
+
+ */
+ }
+
+ /*
+ * if qref is null, "fix" this quaternion
+ * otherwise, return a quaternion that is CLOSEST to the given quaternion
+ * that is, one that gives a positive dot product
+ *
+ */
+ public void setRef(Quat qref) {
+ if (qref == null) {
+ mul(getFixFactor());
+ return;
+ }
+ if (dot(qref) >= 0)
+ return;
+ q0 *= -1;
+ q1 *= -1;
+ q2 *= -1;
+ q3 *= -1;
+ }
+
+ /**
+ * returns a quaternion frame based on three points (center, x, and any point in xy plane)
+ * or two vectors (vA, vB).
+ *
+ * @param center (null for vA/vB option)
+ * @param x
+ * @param xy
+ * @return quaternion for frame
+ */
+ public static final Quat getQuaternionFrame(P3 center, T3 x,
+ T3 xy) {
+ V3 vA = V3.newV(x);
+ V3 vB = V3.newV(xy);
+ if (center != null) {
+ vA.sub(center);
+ vB.sub(center);
+ }
+ return getQuaternionFrameV(vA, vB, null, false);
+ }
+
+ /**
+ * Create a quaternion based on a frame
+ * @param vA
+ * @param vB
+ * @param vC
+ * @param yBased
+ * @return quaternion
+ */
+ public static final Quat getQuaternionFrameV(V3 vA, V3 vB,
+ V3 vC, boolean yBased) {
+ if (vC == null) {
+ vC = new V3();
+ vC.cross(vA, vB);
+ if (yBased)
+ vA.cross(vB, vC);
+ }
+ V3 vBprime = new V3();
+ vBprime.cross(vC, vA);
+ vA.normalize();
+ vBprime.normalize();
+ vC.normalize();
+ M3 mat = new M3();
+ mat.setColumnV(0, vA);
+ mat.setColumnV(1, vBprime);
+ mat.setColumnV(2, vC);
+
+ /*
+ *
+ * Verification tests using Quat4f and AngleAxis4f:
+ *
+ System.out.println("quaternion frame matrix: " + mat);
+
+ Point3f pt2 = new Point3f();
+ mat.transform(Point3f.new3(1, 0, 0), pt2);
+ System.out.println("vA=" + vA + " M(100)=" + pt2);
+ mat.transform(Point3f.new3(0, 1, 0), pt2);
+ System.out.println("vB'=" + vBprime + " M(010)=" + pt2);
+ mat.transform(Point3f.new3(0, 0, 1), pt2);
+ System.out.println("vC=" + vC + " M(001)=" + pt2);
+ Quat4f q4 = new Quat4f();
+ q4.set(mat);
+ System.out.println("----");
+ System.out.println("Quat4f: {" + q4.w + " " + q4.x + " " + q4.y + " " + q4.z + "}");
+ System.out.println("Quat4f: 2xy + 2wz = m10: " + (2 * q4.x * q4.y + 2 * q4.w * q4.z) + " = " + mat.m10);
+
+ */
+
+ Quat q = newM(mat);
+
+ /*
+ System.out.println("Quaternion mat from q \n" + q.getMatrix());
+ System.out.println("Quaternion: " + q.getNormal() + " " + q.getTheta());
+ AxisAngle4f a = new AxisAngle4f();
+ a.set(mat);
+ Vector3f v = Vector3f.new3(a.x, a.y, a.z);
+ v.normalize();
+ System.out.println("angleAxis: " + v + " "+(a.angle/Math.PI * 180));
+ */
+
+ return q;
+ }
+
+ public M3 getMatrix() {
+ if (mat == null)
+ setMatrix();
+ return mat;
+ }
+
+ private void setMatrix() {
+ mat = new M3();
+ // q0 = w, q1 = x, q2 = y, q3 = z
+ mat.m00 = q0 * q0 + q1 * q1 - q2 * q2 - q3 * q3;
+ mat.m01 = 2 * q1 * q2 - 2 * q0 * q3;
+ mat.m02 = 2 * q1 * q3 + 2 * q0 * q2;
+ mat.m10 = 2 * q1 * q2 + 2 * q0 * q3;
+ mat.m11 = q0 * q0 - q1 * q1 + q2 * q2 - q3 * q3;
+ mat.m12 = 2 * q2 * q3 - 2 * q0 * q1;
+ mat.m20 = 2 * q1 * q3 - 2 * q0 * q2;
+ mat.m21 = 2 * q2 * q3 + 2 * q0 * q1;
+ mat.m22 = q0 * q0 - q1 * q1 - q2 * q2 + q3 * q3;
+ }
+
+ public Quat add(float x) {
+ // scalar theta addition (degrees)
+ return newVA(getNormal(), getTheta() + x);
+ }
+
+ public Quat mul(float x) {
+ // scalar theta multiplication
+ return (x == 1 ? new4(q1, q2, q3, q0) :
+ newVA(getNormal(), getTheta() * x));
+ }
+
+ public Quat mulQ(Quat p) {
+ return new4(
+ q0 * p.q1 + q1 * p.q0 + q2 * p.q3 - q3 * p.q2,
+ q0 * p.q2 + q2 * p.q0 + q3 * p.q1 - q1 * p.q3,
+ q0 * p.q3 + q3 * p.q0 + q1 * p.q2 - q2 * p.q1,
+ q0 * p.q0 - q1 * p.q1 - q2 * p.q2 - q3 * p.q3);
+ }
+
+ public Quat div(Quat p) {
+ // unit quaternions assumed -- otherwise would scale by 1/p.dot(p)
+ return mulQ(p.inv());
+ }
+
+ public Quat divLeft(Quat p) {
+ // unit quaternions assumed -- otherwise would scale by 1/p.dot(p)
+ return this.inv().mulQ(p);
+ }
+
+ public float dot(Quat q) {
+ return this.q0 * q.q0 + this.q1 * q.q1 + this.q2 * q.q2 + this.q3 * q.q3;
+ }
+
+ public Quat inv() {
+ return new4(-q1, -q2, -q3, q0);
+ }
+
+ public Quat negate() {
+ return new4(-q1, -q2, -q3, -q0);
+ }
+
+ /**
+ * ensures
+ *
+ * 1) q0 > 0
+ * or
+ * 2) q0 = 0 and q1 > 0
+ * or
+ * 3) q0 = 0 and q1 = 0 and q2 > 0
+ * or
+ * 4) q0 = 0 and q1 = 0 and q2 = 0 and q3 > 0
+ *
+ * @return 1 or -1
+ *
+ */
+
+ private float getFixFactor() {
+ return (q0 < 0 ||
+ q0 == 0 && (q1 < 0 || q1 == 0 && (q2 < 0 || q2 == 0 && q3 < 0)) ? -1 : 1);
+ }
+
+ public V3 getVector(int i) {
+ return getVectorScaled(i, 1f);
+ }
+
+ public V3 getVectorScaled(int i, float scale) {
+ if (i == -1) {
+ scale *= getFixFactor();
+ return V3.new3(q1 * scale, q2 * scale, q3 * scale);
+ }
+ if (mat == null)
+ setMatrix();
+ V3 v = new V3();
+ mat.getColumnV(i, v);
+ if (scale != 1f)
+ v.scale(scale);
+ return v;
+ }
+
+ /**
+ *
+ * @return vector such that 0 <= angle <= 180
+ */
+ public V3 getNormal() {
+ V3 v = getRawNormal(this);
+ v.scale(getFixFactor());
+ return v;
+ }
+
+ private static V3 getRawNormal(Quat q) {
+ V3 v = V3.new3(q.q1, q.q2, q.q3);
+ if (v.length() == 0)
+ return V3.new3(0, 0, 1);
+ v.normalize();
+ return v;
+ }
+
+ /**
+ *
+ * @return 0 <= angle <= 180 in degrees
+ */
+ public float getTheta() {
+ return (float) (Math.acos(Math.abs(q0)) * (2 * 180 / Math.PI));
+ }
+
+ public float getThetaRadians() {
+ return (float) (Math.acos(Math.abs(q0)) * 2);
+ }
+
+ /**
+ *
+ * @param v0
+ * @return vector option closest to v0
+ *
+ */
+ public V3 getNormalDirected(V3 v0) {
+ V3 v = getNormal();
+ if (v.x * v0.x + v.y * v0.y + v.z * v0.z < 0) {
+ v.scale(-1);
+ }
+ return v;
+ }
+
+ public V3 get3dProjection(V3 v3d) {
+ v3d.set(q1, q2, q3);
+ return v3d;
+ }
+
+ /**
+ *
+ * @param axisAngle
+ * @return fill in theta of axisAngle such that
+ */
+ public P4 getThetaDirected(P4 axisAngle) {
+ //fills in .w;
+ float theta = getTheta();
+ V3 v = getNormal();
+ if (axisAngle.x * q1 + axisAngle.y * q2 + axisAngle.z * q3 < 0) {
+ v.scale(-1);
+ theta = -theta;
+ }
+ axisAngle.set4(v.x, v.y, v.z, theta);
+ return axisAngle;
+ }
+
+ /**
+ *
+ * @param vector a vector, same as for getNormalDirected
+ * @return return theta
+ */
+ public float getThetaDirectedV(V3 vector) {
+ //fills in .w;
+ float theta = getTheta();
+ V3 v = getNormal();
+ if (vector.x * q1 + vector.y * q2 + vector.z * q3 < 0) {
+ v.scale(-1);
+ theta = -theta;
+ }
+ return theta;
+ }
+
+ /**
+ * Quaternions are saved as {q1, q2, q3, q0}
+ *
+ * While this may seem odd, it is so that for any point4 --
+ * planes, axisangles, and quaternions -- we can use the
+ * first three coordinates to determine the relavent axis
+ * the fourth then gives us offset to {0,0,0} (plane),
+ * rotation angle (axisangle), and cos(theta/2) (quaternion).
+ * @return {x y z w} (unnormalized)
+ */
+ public P4 toPoint4f() {
+ return P4.new4(q1, q2, q3, q0); // x,y,z,w
+ }
+
+ public A4 toAxisAngle4f() {
+ double theta = 2 * Math.acos(Math.abs(q0));
+ double sinTheta2 = Math.sin(theta/2);
+ V3 v = getNormal();
+ if (sinTheta2 < 0) {
+ v.scale(-1);
+ theta = Math.PI - theta;
+ }
+ return A4.newVA(v, (float) theta);
+ }
+
+ public T3 transform2(T3 pt, T3 ptNew) {
+ if (mat == null)
+ setMatrix();
+ mat.rotate2(pt, ptNew);
+ return ptNew;
+ }
+
+ public Quat leftDifference(Quat q2) {
+ //dq = q.leftDifference(qnext);//q.inv().mul(qnext);
+ Quat q2adjusted = (this.dot(q2) < 0 ? q2.negate() : q2);
+ return inv().mulQ(q2adjusted);
+ }
+
+ public Quat rightDifference(Quat q2) {
+ //dq = qnext.rightDifference(q);//qnext.mul(q.inv());
+ Quat q2adjusted = (this.dot(q2) < 0 ? q2.negate() : q2);
+ return mulQ(q2adjusted.inv());
+ }
+
+ /**
+ *
+ * Java axisAngle / plane / Point4f format
+ * all have the format {x y z w}
+ * so we go with that here as well
+ *
+ * @return "{q1 q2 q3 q0}"
+ */
+ @Override
+ public String toString() {
+ return "{" + q1 + " " + q2 + " " + q3 + " " + q0 + "}";
+ }
+
+ /**
+ *
+ * @param data1
+ * @param data2
+ * @param nMax > 0 --> limit to this number
+ * @param isRelative
+ *
+ * @return pairwise array of data1 / data2 or data1 \ data2
+ */
+ public static Quat[] div(Quat[] data1, Quat[] data2, int nMax, boolean isRelative) {
+ int n;
+ if (data1 == null || data2 == null || (n = Math.min(data1.length, data2.length)) == 0)
+ return null;
+ if (nMax > 0 && n > nMax)
+ n = nMax;
+ Quat[] dqs = new Quat[n];
+ for (int i = 0; i < n; i++) {
+ if (data1[i] == null || data2[i] == null)
+ return null;
+ dqs[i] = (isRelative ? data1[i].divLeft(data2[i]) : data1[i].div(data2[i]));
+ }
+ return dqs;
+ }
+
+ public static Quat sphereMean(Quat[] data, float[] retStddev, float criterion) {
+ // Samuel R. Buss, Jay P. Fillmore:
+ // Spherical averages and applications to spherical splines and interpolation.
+ // ACM Trans. Graph. 20(2): 95-126 (2001)
+ if (data == null || data.length == 0)
+ return new Quat();
+ if (retStddev == null)
+ retStddev = new float[1];
+ if (data.length == 1) {
+ retStddev[0] = 0;
+ return newQ(data[0]);
+ }
+ float diff = Float.MAX_VALUE;
+ float lastStddev = Float.MAX_VALUE;
+ Quat qMean = simpleAverage(data);
+ int maxIter = 100; // typically goes about 5 iterations
+ int iter = 0;
+ while (diff > criterion && lastStddev != 0 && iter < maxIter) {
+ qMean = newMean(data, qMean);
+ retStddev[0] = stdDev(data, qMean);
+ diff = Math.abs(retStddev[0] - lastStddev);
+ lastStddev = retStddev[0];
+ //Logger.info(++iter + " sphereMean " + qMean + " stddev=" + lastStddev + " diff=" + diff);
+ }
+ return qMean;
+ }
+
+ /**
+ * Just a starting point.
+ * get average normal vector
+ * scale normal by average projection of vectors onto it
+ * create quaternion from this 3D projection
+ *
+ * @param ndata
+ * @return approximate average
+ */
+ private static Quat simpleAverage(Quat[] ndata) {
+ V3 mean = V3.new3(0, 0, 1);
+ // using the directed normal ensures that the mean is
+ // continually added to and never subtracted from
+ V3 v = ndata[0].getNormal();
+ mean.add(v);
+ for (int i = ndata.length; --i >= 0;)
+ mean.add(ndata[i].getNormalDirected(mean));
+ mean.sub(v);
+ mean.normalize();
+ float f = 0;
+ // the 3D projection of the quaternion is [sin(theta/2)]*n
+ // so dotted with the normalized mean gets us an approximate average for sin(theta/2)
+ for (int i = ndata.length; --i >= 0;)
+ f += Math.abs(ndata[i].get3dProjection(v).dot(mean));
+ if (f != 0)
+ mean.scale(f / ndata.length);
+ // now convert f to the corresponding cosine instead of sine
+ f = (float) Math.sqrt(1 - mean.lengthSquared());
+ if (Float.isNaN(f))
+ f = 0;
+ return newP4(P4.new4(mean.x, mean.y, mean.z, f));
+ }
+
+ private static Quat newMean(Quat[] data, Quat mean) {
+ /* quaternion derivatives nicely take care of producing the necessary
+ * metric. Since dq gives us the normal with the smallest POSITIVE angle,
+ * we just scale by that -- using degrees.
+ * No special normalization is required.
+ *
+ * The key is that the mean has been set up already, and dq.getTheta()
+ * will always return a value between 0 and 180. True, for groupings
+ * where dq swings wildly -- 178, 182, 178, for example -- there will
+ * be problems, but the presumption here is that there is a REASONABLE
+ * set of data. Clearly there are spherical data sets that simply cannot
+ * be assigned a mean. (For example, where the three projected points
+ * are equally distant on the sphere. We just can't worry about those
+ * cases here. Rather, if there is any significance to the data,
+ * there will be clusters of projected points, and the analysis will
+ * be meaningful.
+ *
+ * Note that the hemisphere problem drops out because dq.getNormal() and
+ * dq.getTheta() will never return (n, 182 degrees) but will
+ * instead return (-n, 2 degrees). That's just what we want in that case.
+ *
+ * Note that the projection in this case is to 3D -- a set of vectors
+ * in space with lengths proportional to theta (not the sin(theta/2)
+ * that is associated with a quaternion map).
+ *
+ * This is officially an "exponential" or "hyperbolic" projection.
+ *
+ */
+ V3 sum = new V3();
+ V3 v;
+ Quat q, dq;
+ //System.out.println("newMean mean " + mean);
+ for (int i = data.length; --i >= 0;) {
+ q = data[i];
+ dq = q.div(mean);
+ v = dq.getNormal();
+ v.scale(dq.getTheta());
+ sum.add(v);
+ }
+ sum.scale(1f/data.length);
+ Quat dqMean = newVA(sum, sum.length());
+ //System.out.println("newMean dqMean " + dqMean + " " + dqMean.getNormal() + " " + dqMean.getTheta());
+ return dqMean.mulQ(mean);
+ }
+
+ /**
+ * @param data
+ * @param mean
+ * @return standard deviation in units of degrees
+ */
+ private static float stdDev(Quat[] data, Quat mean) {
+ // the quaternion dot product gives q0 for dq (i.e. q / mean)
+ // that is, cos(theta/2) for theta between them
+ double sum2 = 0;
+ int n = data.length;
+ for (int i = n; --i >= 0;) {
+ float theta = data[i].div(mean).getTheta();
+ sum2 += theta * theta;
+ }
+ return (float) Math.sqrt(sum2 / n);
+ }
+
+ public float[] getEulerZYZ() {
+ // http://www.swarthmore.edu/NatSci/mzucker1/e27/diebel2006attitude.pdf
+ double rA, rB, rG;
+ if (q1 == 0 && q2 == 0) {
+ float theta = getTheta();
+ // pure Z rotation - ambiguous
+ return new float[] { q3 < 0 ? -theta : theta , 0, 0 };
+ }
+ rA = Math.atan2(2 * (q2 * q3 + q0 * q1), 2 * (-q1 * q3 + q0 * q2 ));
+ rB = Math.acos(q3 * q3 - q2 * q2 - q1 * q1 + q0 * q0);
+ rG = Math.atan2( 2 * (q2 * q3 - q0 * q1), 2 * (q0 * q2 + q1 * q3));
+ return new float[] {(float) (rA / RAD_PER_DEG), (float) (rB / RAD_PER_DEG), (float) (rG / RAD_PER_DEG)};
+ }
+
+ public float[] getEulerZXZ() {
+ // NOT http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
+ // http://www.swarthmore.edu/NatSci/mzucker1/e27/diebel2006attitude.pdf
+ double rA, rB, rG;
+ if (q1 == 0 && q2 == 0) {
+ float theta = getTheta();
+ // pure Z rotation - ambiguous
+ return new float[] { q3 < 0 ? -theta : theta , 0, 0 };
+ }
+ rA = Math.atan2(2 * (q1 * q3 - q0 * q2), 2 * (q0 * q1 + q2 * q3 ));
+ rB = Math.acos(q3 * q3 - q2 * q2 - q1 * q1 + q0 * q0);
+ rG = Math.atan2( 2 * (q1 * q3 + q0 * q2), 2 * (-q2 * q3 + q0 * q1));
+ return new float[] {(float) (rA / RAD_PER_DEG), (float) (rB / RAD_PER_DEG), (float) (rG / RAD_PER_DEG)};
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-04-05 09:07:28 -0500 (Thu, 05 Apr 2007) $
+ * $Revision: 7326 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 javajs.util;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.StringReader;
+import java.io.UnsupportedEncodingException;
+
+import java.util.Map;
+
+import javajs.api.Interface;
+
+
+import javajs.J2SIgnoreImport;
+import javajs.api.GenericCifDataParser;
+import javajs.api.GenericLineReader;
+import javajs.api.GenericZipTools;
+
+/**
+ * A general helper class for a variety of stream and reader functionality
+ * including:
+ *
+ * stream and byte magic-number decoding for PNG, PNGJ, ZIP, and GZIP streams
+ *
+ * various stream/reader methods, including UTF-encoded stream reading
+ *
+ * reflection-protected access to a CIF parser and ZIP tools
+ *
+ *
+ *
+ *
+ */
+@J2SIgnoreImport(BufferedWriter.class)
+public class Rdr implements GenericLineReader {
+
+ BufferedReader reader;
+
+ public Rdr(BufferedReader reader) {
+ this.reader = reader;
+ }
+
+ @Override
+ public String readNextLine() throws Exception {
+ return reader.readLine();
+ }
+
+ public static Map<String, Object> readCifData(GenericCifDataParser parser, BufferedReader br) {
+ return parser.set(null, br, false).getAllCifData();
+ }
+
+
+ ///////////
+
+
+ /**
+ *
+ * Read a UTF-8 byte array fully, converting it to a String.
+ * Called by Jmol's XMLReaders
+ *
+ * @param bis
+ * @return a UTF-8 string
+ */
+ public static String bytesToUTF8String(byte[] bytes) {
+ return streamToUTF8String(new BufferedInputStream(new ByteArrayInputStream(bytes)));
+ }
+
+ /**
+ *
+ * Read a UTF-8 stream fully, converting it to a String.
+ * Called by Jmol's XMLReaders
+ *
+ * @param bis
+ * @return a UTF-8 string
+ */
+ public static String streamToUTF8String(BufferedInputStream bis) {
+ String[] data = new String[1];
+ try {
+ readAllAsString(getBufferedReader(bis, "UTF-8"), -1, true, data, 0);
+ } catch (IOException e) {
+ }
+ return data[0];
+ }
+
+ /**
+ * Read an input stream fully, saving a byte array, then
+ * return a buffered reader to those bytes converted to string form.
+ *
+ * @param bis
+ * @param charSet
+ * @return Reader
+ * @throws IOException
+ */
+ public static BufferedReader getBufferedReader(BufferedInputStream bis, String charSet)
+ throws IOException {
+ // could also just make sure we have a buffered input stream here.
+ if (getUTFEncodingForStream(bis) == Encoding.NONE)
+ return new BufferedReader(new InputStreamReader(bis, (charSet == null ? "UTF-8" : charSet)));
+ byte[] bytes = getLimitedStreamBytes(bis, -1);
+ bis.close();
+ return getBR(charSet == null ? fixUTF(bytes) : new String(bytes, charSet));
+ }
+
+ /**
+ * This method is specifically for strings that are marked for UTF 8 or 16.
+ *
+ * @param bytes
+ * @return
+ */
+ public static String fixUTF(byte[] bytes) {
+ Encoding encoding = getUTFEncoding(bytes);
+ if (encoding != Encoding.NONE)
+ try {
+ String s = new String(bytes, encoding.name().replace('_', '-'));
+ switch (encoding) {
+ case UTF8:
+ case UTF_16BE:
+ case UTF_16LE:
+ // extra byte at beginning removed
+ s = s.substring(1);
+ break;
+ default:
+ break;
+ }
+ return s;
+ } catch (UnsupportedEncodingException e) {
+ System.out.println(e);
+ }
+ return new String(bytes);
+ }
+
+ private static Encoding getUTFEncoding(byte[] bytes) {
+ if (bytes.length >= 3 && (bytes[0] & 0xFF) == 0xEF && (bytes[1] & 0xFF) == 0xBB && (bytes[2] & 0xFF) == 0xBF)
+ return Encoding.UTF8;
+ if (bytes.length >= 4 && (bytes[0] & 0xFF) == 0 && (bytes[1] & 0xFF) == 0
+ && (bytes[2] & 0xFF) == 0xFE && (bytes[3] & 0xFF) == 0xFF)
+ return Encoding.UTF_32BE;
+ if (bytes.length >= 4 && (bytes[0] & 0xFF) == 0xFF && (bytes[1] & 0xFF) == 0xFE
+ && (bytes[2] & 0xFF) == 0 && (bytes[3] & 0xFF) == 0)
+ return Encoding.UTF_32LE;
+ if (bytes.length >= 2 && (bytes[0] & 0xFF) == 0xFF && (bytes[1] & 0xFF) == 0xFE)
+ return Encoding.UTF_16LE;
+ if (bytes.length >= 2 && (bytes[0] & 0xFF) == 0xFE && (bytes[1] & 0xFF) == 0xFF)
+ return Encoding.UTF_16BE;
+ return Encoding.NONE;
+
+ }
+
+ ////////// stream type checking //////////
+
+
+ private static Encoding getUTFEncodingForStream(BufferedInputStream is) throws IOException {
+ /**
+ * @j2sNative
+ *
+ * is.resetStream();
+ *
+ */
+ {
+ }
+ byte[] abMagic = new byte[4];
+ abMagic[3] = 1;
+ try{
+ is.mark(5);
+ } catch (Exception e) {
+ return Encoding.NONE;
+ }
+ is.read(abMagic, 0, 4);
+ is.reset();
+ return getUTFEncoding(abMagic);
+ }
+
+ public static boolean isBase64(SB sb) {
+ return (sb.indexOf(";base64,") == 0);
+ }
+
+ public static boolean isCompoundDocumentS(InputStream is) {
+ return isCompoundDocumentB(getMagic(is, 8));
+ }
+
+ public static boolean isCompoundDocumentB(byte[] bytes) {
+ return (bytes.length >= 8 && (bytes[0] & 0xFF) == 0xD0
+ && (bytes[1] & 0xFF) == 0xCF && (bytes[2] & 0xFF) == 0x11
+ && (bytes[3] & 0xFF) == 0xE0 && (bytes[4] & 0xFF) == 0xA1
+ && (bytes[5] & 0xFF) == 0xB1 && (bytes[6] & 0xFF) == 0x1A
+ && (bytes[7] & 0xFF) == 0xE1);
+ }
+
+ public static boolean isGzipS(InputStream is) {
+ return isGzipB(getMagic(is, 2));
+ }
+
+ public static boolean isGzipB(byte[] bytes) {
+ return (bytes != null && bytes.length >= 2
+ && (bytes[0] & 0xFF) == 0x1F && (bytes[1] & 0xFF) == 0x8B);
+ }
+
+ public static boolean isPickleS(InputStream is) {
+ return isPickleB(getMagic(is, 2));
+ }
+
+ public static boolean isPickleB(byte[] bytes) {
+ return (bytes != null && bytes.length >= 2
+ && (bytes[0] & 0xFF) == 0x7D && (bytes[1] & 0xFF) == 0x71);
+ }
+
+ public static boolean isMessagePackS(InputStream is) {
+ return isMessagePackB(getMagic(is, 1));
+ }
+
+ public static boolean isMessagePackB(byte[] bytes) {
+ // look for 'map' start
+ return (bytes != null && bytes.length >= 1 && (bytes[0] & 0xFF) == 0xDE);
+ }
+
+ public static boolean isPngZipStream(InputStream is) {
+ return isPngZipB(getMagic(is, 55));
+ }
+
+ public static boolean isPngZipB(byte[] bytes) {
+ // \0PNGJ starting at byte 50
+ return (bytes[50] == 0 && bytes[51] == 0x50 && bytes[52] == 0x4E && bytes[53] == 0x47 && bytes[54] == 0x4A);
+ }
+
+ public static boolean isZipS(InputStream is) {
+ return isZipB(getMagic(is, 4));
+ }
+
+ public static boolean isZipB(byte[] bytes) {
+ return (bytes.length >= 4
+ && bytes[0] == 0x50 //PK<03><04>
+ && bytes[1] == 0x4B
+ && bytes[2] == 0x03
+ && bytes[3] == 0x04);
+ }
+
+ public static byte[] getMagic(InputStream is, int n) {
+ byte[] abMagic = new byte[n];
+ /**
+ * @j2sNative
+ *
+ * is.resetStream();
+ *
+ */
+ {
+ }
+ try {
+ is.mark(n + 1);
+ is.read(abMagic, 0, n);
+ } catch (IOException e) {
+ }
+ try {
+ is.reset();
+ } catch (IOException e) {
+ }
+ return abMagic;
+ }
+
+ public static String guessMimeTypeForBytes(byte[] bytes) {
+ // only options here are JPEG, PNG, GIF, and BMP
+ switch (bytes.length < 2 ? -1 : bytes[1]) {
+ case 0:
+ return "image/jpg"; // 0xFF 0x00 ...
+ case 0x49:
+ return "image/gif"; // GIF89a...
+ case 0x4D:
+ return "image/BMP"; // BM...
+ case 0x50:
+ return "image/png";
+ default:
+ return "image/unknown";
+ }
+ }
+
+
+ ////////// stream/byte methods ///////////
+
+ public static BufferedInputStream getBIS(byte[] bytes) {
+ return new BufferedInputStream(new ByteArrayInputStream(bytes));
+ }
+
+ public static BufferedReader getBR(String string) {
+ return new BufferedReader(new StringReader(string));
+ }
+
+ /**
+ * Drill down into a GZIP stack until no more layers.
+ * @param jzt
+ *
+ * @param bis
+ * @return non-gzipped buffered input stream.
+ *
+ * @throws IOException
+ */
+ public static BufferedInputStream getUnzippedInputStream(GenericZipTools jzt, BufferedInputStream bis) throws IOException {
+ while (isGzipS(bis))
+ bis = new BufferedInputStream(jzt.newGZIPInputStream(bis));
+ return bis;
+ }
+
+ /**
+ * Allow for base64-encoding check.
+ *
+ * @param sb
+ * @return byte array
+ */
+ public static byte[] getBytesFromSB(SB sb) {
+ return (isBase64(sb) ? Base64.decodeBase64(sb.substring(8)) : sb.toBytes(0, -1));
+ }
+
+ /**
+ * Read a an entire BufferedInputStream for its bytes, and
+ * either return them or leave them in the designated output channel.
+ *
+ * @param bis
+ * @param out a destination output channel, or null
+ * @return byte[] (if out is null) or a message indicating length (if not)
+ *
+ * @throws IOException
+ */
+ public static Object getStreamAsBytes(BufferedInputStream bis,
+ OC out) throws IOException {
+ byte[] buf = new byte[1024];
+ byte[] bytes = (out == null ? new byte[4096] : null);
+ int len = 0;
+ int totalLen = 0;
+ while ((len = bis.read(buf, 0, 1024)) > 0) {
+ totalLen += len;
+ if (out == null) {
+ if (totalLen >= bytes.length)
+ bytes = AU.ensureLengthByte(bytes, totalLen * 2);
+ System.arraycopy(buf, 0, bytes, totalLen - len, len);
+ } else {
+ out.write(buf, 0, len);
+ }
+ }
+ bis.close();
+ if (out == null) {
+ return AU.arrayCopyByte(bytes, totalLen);
+ }
+ return totalLen + " bytes";
+ }
+
+ /**
+ * Read a possibly limited number of bytes (when n > 0) from a stream,
+ * leaving the stream open.
+ *
+ * @param is an input stream, not necessarily buffered.
+ * @param n the maximum number of bytes to read, or -1 for all
+ * @return the bytes read
+ *
+ * @throws IOException
+ */
+ public static byte[] getLimitedStreamBytes(InputStream is, long n)
+ throws IOException {
+
+ //Note: You cannot use InputStream.available() to reliably read
+ // zip data from the web.
+
+ int buflen = (n > 0 && n < 1024 ? (int) n : 1024);
+ byte[] buf = new byte[buflen];
+ byte[] bytes = new byte[n < 0 ? 4096 : (int) n];
+ int len = 0;
+ int totalLen = 0;
+ if (n < 0)
+ n = Integer.MAX_VALUE;
+ while (totalLen < n && (len = is.read(buf, 0, buflen)) > 0) {
+ totalLen += len;
+ if (totalLen > bytes.length)
+ bytes = AU.ensureLengthByte(bytes, totalLen * 2);
+ System.arraycopy(buf, 0, bytes, totalLen - len, len);
+ if (n != Integer.MAX_VALUE && totalLen + buflen > bytes.length)
+ buflen = bytes.length - totalLen;
+
+ }
+ if (totalLen == bytes.length)
+ return bytes;
+ buf = new byte[totalLen];
+ System.arraycopy(bytes, 0, buf, 0, totalLen);
+ return buf;
+ }
+
+ /**
+ * This method fills data[i] with string data from a file that may or may not
+ * be binary even though it is being read by a reader. It is meant to be used
+ * simple text-based files only.
+ *
+ * @param br
+ * @param nBytesMax
+ * @param allowBinary
+ * @param data
+ * @param i
+ * @return true if data[i] holds the data; false if data[i] holds an error message.
+ */
+ public static boolean readAllAsString(BufferedReader br, int nBytesMax, boolean allowBinary, String[] data, int i) {
+ try {
+ SB sb = SB.newN(8192);
+ String line;
+ if (nBytesMax < 0) {
+ line = br.readLine();
+ if (allowBinary || line != null && line.indexOf('\0') < 0
+ && (line.length() != 4 || line.charAt(0) != 65533
+ || line.indexOf("PNG") != 1)) {
+ sb.append(line).appendC('\n');
+ while ((line = br.readLine()) != null)
+ sb.append(line).appendC('\n');
+ }
+ } else {
+ int n = 0;
+ int len;
+ while (n < nBytesMax && (line = br.readLine()) != null) {
+ if (nBytesMax - n < (len = line.length()) + 1)
+ line = line.substring(0, nBytesMax - n - 1);
+ sb.append(line).appendC('\n');
+ n += len + 1;
+ }
+ }
+ br.close();
+ data[i] = sb.toString();
+ return true;
+ } catch (Exception ioe) {
+ data[i] = ioe.toString();
+ return false;
+ }
+ }
+
+
+ /////////// PNGJ support /////////////
+
+
+ /**
+ * Look at byte 50 for "\0PNGJxxxxxxxxx+yyyyyyyyy" where xxxxxxxxx is a byte
+ * offset to the JMOL data and yyyyyyyyy is the length of the data.
+ *
+ * @param bis
+ * @return same stream or byte stream
+ */
+
+ /**
+ * Retrieve the two numbers in a PNG iTXt tag indicating the
+ * file pointer for the start of the ZIP data as well as its length.
+ *
+ * @param bis
+ * @param pt_count
+ */
+ static void getPngZipPointAndCount(BufferedInputStream bis, int[] pt_count) {
+ bis.mark(75);
+ try {
+ byte[] data = getLimitedStreamBytes(bis, 74);
+ bis.reset();
+ int pt = 0;
+ for (int i = 64, f = 1; --i > 54; f *= 10)
+ pt += (data[i] - '0') * f;
+ int n = 0;
+ for (int i = 74, f = 1; --i > 64; f *= 10)
+ n += (data[i] - '0') * f;
+ pt_count[0] = pt;
+ pt_count[1] = n;
+ } catch (Throwable e) {
+ pt_count[1] = 0;
+ }
+ }
+
+ /**
+ * Either advance a PNGJ stream to its zip file data or pull out the ZIP data
+ * bytes and create a new stream for them from which a ZIP utility can start
+ * extracting files.
+ *
+ * @param bis
+ * @param asNewStream
+ * @return new buffered ByteArrayInputStream, possibly with no data if there is an error
+ */
+ public static BufferedInputStream getPngZipStream(BufferedInputStream bis, boolean asNewStream) {
+ if (!isPngZipStream(bis))
+ return bis;
+ byte[] data = new byte[0];
+ bis.mark(75);
+ try {
+ int pt_count[] = new int[2];
+ getPngZipPointAndCount(bis, pt_count);
+ if (pt_count[1] != 0) {
+ int pt = pt_count[0];
+ while (pt > 0)
+ pt -= bis.skip(pt);
+ if (!asNewStream)
+ return bis;
+ data = getLimitedStreamBytes(bis, pt_count[1]);
+ }
+ } catch (Throwable e) {
+ } finally {
+ try {
+ if (asNewStream)
+ bis.close();
+ } catch (Exception e) {
+ // ignore
+ }
+ }
+ return getBIS(data);
+ }
+
+ /** We define a request for zip file extraction by vertical bar:
+ * zipName|interiorFileName. These may be nested if there is a
+ * zip file contained in a zip file.
+ *
+ * @param fileName
+ * @return filename trimmed of interior fileName
+ *
+ */
+ public static String getZipRoot(String fileName) {
+ int pt = fileName.indexOf("|");
+ return (pt < 0 ? fileName : fileName.substring(0, pt));
+ }
+
+ public static BufferedWriter getBufferedWriter(OutputStream os, String charSetName) {
+ OutputStreamWriter osw = (OutputStreamWriter) Interface.getInstanceWithParams("java.io.OutputStreamWriter",
+ new Class<?>[] { java.io.OutputStream.class, String.class }, new Object[] {os, charSetName});
+ /**
+ * @j2sNative
+ * return osw.getBufferedWriter();
+ *
+ */
+ {
+ return new BufferedWriter(osw);
+ }
+ }
+
+
+}
+
--- /dev/null
+
+package javajs.util;
+
+import java.nio.charset.Charset;
+
+import javajs.J2SIgnoreImport;
+
+/**
+ * Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
+ *
+ * Java StringBuilder is final, unfortunately. I guess they weren't thinking about Java2Script!
+ *
+ * The reason we have to do this that several overloaded append methods is WAY too expensive
+ *
+ */
+
+@J2SIgnoreImport({java.lang.StringBuilder.class, java.nio.charset.Charset.class})
+public class SB {
+
+ private java.lang.StringBuilder sb;
+ String s; // used by JavaScript only; no Java references
+
+ //TODO: JS experiment with using array and .push() here
+
+ public SB() {
+ /**
+ * @j2sNative
+ *
+ * this.s = "";
+ *
+ */
+ {
+ sb = new java.lang.StringBuilder();
+ }
+ }
+
+ public static SB newN(int n) {
+ /**
+ * @j2sNative
+ * return new javajs.util.SB();
+ */
+ {
+ // not perfect, because it requires defining sb twice.
+ // We can do better...
+ SB sb = new SB();
+ sb.sb = new java.lang.StringBuilder(n);
+ return sb;
+ }
+ }
+
+ public static SB newS(String s) {
+ /**
+ * @j2sNative
+ *
+ * var sb = new javajs.util.SB();
+ * sb.s = s;
+ * return sb;
+ *
+ */
+ {
+ SB sb = new SB();
+ sb.sb = new java.lang.StringBuilder(s);
+ return sb;
+ }
+ }
+
+ public SB append(String s) {
+ /**
+ * @j2sNative
+ *
+ * this.s += s
+ *
+ */
+ {
+ sb.append(s);
+ }
+ return this;
+ }
+
+ public SB appendC(char c) {
+ /**
+ * @j2sNative
+ *
+ * this.s += c;
+ */
+ {
+ sb.append(c);
+ }
+ return this;
+
+ }
+
+ public SB appendI(int i) {
+ /**
+ * @j2sNative
+ *
+ * this.s += i
+ *
+ */
+ {
+ sb.append(i);
+ }
+ return this;
+ }
+
+ public SB appendB(boolean b) {
+ /**
+ * @j2sNative
+ *
+ * this.s += b
+ *
+ */
+ {
+ sb.append(b);
+ }
+ return this;
+ }
+
+ /**
+ * note that JavaScript could drop off the ".0" in "1.0"
+ * @param f
+ * @return this
+ */
+ public SB appendF(float f) {
+ /**
+ * @j2sNative
+ *
+ * var sf = "" + f;
+ * if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0)
+ * sf += ".0" ;
+ * this.s += sf;
+ *
+ */
+ {
+ sb.append(f);
+ }
+ return this;
+ }
+
+ public SB appendD(double d) {
+ /**
+ * @j2sNative
+ *
+ * var sf = "" + d;
+ * if (sf.indexOf(".") < 0 && sf.indexOf("e") < 0)
+ * sf += ".0" ;
+ * this.s += sf;
+ *
+ */
+ {
+ sb.append(d);
+ }
+ return this;
+ }
+
+ public SB appendSB(SB buf) {
+ /**
+ * @j2sNative
+ *
+ * this.s += buf.s;
+ *
+ */
+ {
+ sb.append(buf.sb);
+ }
+ return this;
+ }
+
+ public SB appendO(Object data) {
+ if (data != null) {
+ /**
+ * @j2sNative
+ *
+ * this.s += data.toString();
+ *
+ */
+ {
+ sb.append(data);
+ }
+ }
+ return this;
+ }
+
+ public void appendCB(char[] cb, int off, int len) {
+ /**
+ * @j2sNative
+ *
+ * this.s += cb.slice(off,off+len).join("");
+ *
+ */
+ {
+ sb.append(cb, off, len);
+ }
+ }
+
+ @Override
+ public String toString() {
+ /**
+ * @j2sNative
+ *
+ * return this.s;
+ *
+ */
+ {
+ return sb.toString();
+ }
+ }
+
+ public int length() {
+ /**
+ * @j2sNative
+ *
+ * return this.s.length;
+ *
+ */
+ {
+ return sb.length();
+ }
+ }
+
+ public int indexOf(String s) {
+ /**
+ * @j2sNative
+ *
+ * return this.s.indexOf(s);
+ *
+ */
+ {
+ return sb.indexOf(s);
+ }
+ }
+
+ public char charAt(int i) {
+ /**
+ * @j2sNative
+ *
+ * return this.s.charAt(i);
+ *
+ */
+ {
+ return sb.charAt(i);
+ }
+ }
+
+ public int charCodeAt(int i) {
+ /**
+ * @j2sNative
+ *
+ * return this.s.charCodeAt(i);
+ *
+ */
+ {
+ return sb.codePointAt(i);
+ }
+ }
+
+ public void setLength(int n) {
+ /**
+ * @j2sNative
+ *
+ * this.s = this.s.substring(0, n);
+ */
+ {
+ sb.setLength(n);
+ }
+ }
+
+ public int lastIndexOf(String s) {
+ /**
+ * @j2sNative
+ *
+ * return this.s.lastIndexOf(s);
+ */
+ {
+ return sb.lastIndexOf(s);
+ }
+ }
+
+ public int indexOf2(String s, int i) {
+ /**
+ * @j2sNative
+ *
+ * return this.s.indexOf(s, i);
+ */
+ {
+ return sb.indexOf(s, i);
+ }
+ }
+
+ public String substring(int i) {
+ /**
+ * @j2sNative
+ *
+ * return this.s.substring(i);
+ */
+ {
+ return sb.substring(i);
+ }
+ }
+
+ public String substring2(int i, int j) {
+ /**
+ * @j2sNative
+ *
+ * return this.s.substring(i, j);
+ */
+ {
+ return sb.substring(i, j);
+ }
+ }
+
+ /**
+ * simple byte conversion properly implementing UTF-8.
+ * Used for base64 conversion and allows for offset
+ *
+ * @param off
+ * @param len
+ * or -1 for full length (then off must = 0)
+ * @return byte[]
+ */
+ public byte[] toBytes(int off, int len) {
+ if (len == 0)
+ return new byte[0];
+ Charset cs;
+ /**
+ *
+ * just a string in JavaScript
+ *
+ * @j2sNative
+ *
+ * cs = "UTF-8";
+ *
+ */
+ {
+ cs = Charset.forName("UTF-8");
+ }
+ return (len > 0 ? substring2(off, off + len)
+ : off == 0 ? toString()
+ : substring2(off, length() - off)).getBytes(cs);
+ }
+
+ public void replace(int start, int end, String str) {
+ /**
+ * @j2sNative
+ *
+ * this.s = this.s.substring(0, start) + str + this.s.substring(end);
+ */
+ {
+ sb.replace(start, end, str);
+ }
+ }
+
+ public void insert(int offset, String str) {
+ replace(offset, offset, str);
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2011 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package javajs.util;
+
+import java.io.StringReader;
+
+
+
+
+
+public class StringDataReader extends DataReader {
+
+ public StringDataReader() {
+ super();
+ }
+
+ public StringDataReader(String data) {
+ super(new StringReader(data));
+ }
+
+ @Override
+ public DataReader setData(Object data) {
+ return new StringDataReader((String) data);
+ }
+}
\ No newline at end of file
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+import javajs.api.JSONEncodable;
+
+/**
+ * A generic 3 element tuple that is represented by single precision floating
+ * point x,y and z coordinates.
+ *
+ * @version specification 1.1, implementation $Revision: 1.10 $, $Date:
+ * 2006/09/08 20:20:20 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012
+ * for unique constructor and method names
+ * for the optimization of compiled JavaScript using Java2Script.
+ *
+ */
+public abstract class T3 implements JSONEncodable {
+
+ public float x, y, z;
+
+ /**
+ * Sets the value of this tuple to the specified xyz coordinates.
+ *
+ * @param x
+ * the x coordinate
+ * @param y
+ * the y coordinate
+ * @param z
+ * the z coordinate
+ */
+ public final void set(float x, float y, float z) {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ }
+
+ /**
+ * Sets the value of this tuple from the 3 values specified in the array.
+ *
+ * @param t
+ * the array of length 3 containing xyz in order
+ */
+ public final void setA(float t[]) {
+ // ArrayIndexOutOfBounds is thrown if t.length < 3
+ x = t[0];
+ y = t[1];
+ z = t[2];
+ }
+
+ /**
+ * Sets the value of this tuple to the value of the Tuple3f argument.
+ *
+ * @param t1
+ * the tuple to be copied
+ */
+ public final void setT(T3 t1) {
+ x = t1.x;
+ y = t1.y;
+ z = t1.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the vector sum of tuples t1 and t2.
+ *
+ * @param t1
+ * the first tuple
+ * @param t2
+ * the second tuple
+ */
+ public final void add2(T3 t1, T3 t2) {
+ x = t1.x + t2.x;
+ y = t1.y + t2.y;
+ z = t1.z + t2.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the vector sum of itself and tuple t1.
+ *
+ * @param t1
+ * the other tuple
+ */
+ public final void add(T3 t1) {
+ x += t1.x;
+ y += t1.y;
+ z += t1.z;
+ }
+
+ /**
+ * Computes the square of the distance between this point and point p1.
+ *
+ * @param p1
+ * the other point
+ * @return the square of distance between these two points as a float
+ */
+ public final float distanceSquared(T3 p1) {
+ double dx = x - p1.x;
+ double dy = y - p1.y;
+ double dz = z - p1.z;
+ return (float) (dx * dx + dy * dy + dz * dz);
+ }
+
+ /**
+ * Returns the distance between this point and point p1.
+ *
+ * @param p1
+ * the other point
+ * @return the distance between these two points
+ */
+ public final float distance(T3 p1) {
+ return (float) Math.sqrt(distanceSquared(p1));
+ }
+
+ /**
+ * Sets the value of this tuple to the vector difference of tuple t1 and t2
+ * (this = t1 - t2).
+ *
+ * @param t1
+ * the first tuple
+ * @param t2
+ * the second tuple
+ */
+ public final void sub2(T3 t1, T3 t2) {
+ x = t1.x - t2.x;
+ y = t1.y - t2.y;
+ z = t1.z - t2.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the vector difference of itself and tuple
+ * t1 (this = this - t1).
+ *
+ * @param t1
+ * the other tuple
+ */
+ public final void sub(T3 t1) {
+ x -= t1.x;
+ y -= t1.y;
+ z -= t1.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the scalar multiplication of itself.
+ *
+ * @param s
+ * the scalar value
+ */
+ public final void scale(float s) {
+ x *= s;
+ y *= s;
+ z *= s;
+ }
+
+ /**
+ * Add {a b c}
+ *
+ * @param a
+ * @param b
+ * @param c
+ */
+ public final void add3(float a, float b, float c) {
+ x += a;
+ y += b;
+ z += c;
+ }
+
+
+ /**
+ * {x*p.x, y*p.y, z*p.z) used for three-way scaling
+ *
+ * @param p
+ */
+ public final void scaleT(T3 p) {
+ x *= p.x;
+ y *= p.y;
+ z *= p.z;
+ }
+
+
+ /**
+ * Sets the value of this tuple to the scalar multiplication of tuple t1 and
+ * then adds tuple t2 (this = s*t1 + t2).
+ *
+ * @param s
+ * the scalar value
+ * @param t1
+ * the tuple to be multipled
+ * @param t2
+ * the tuple to be added
+ */
+ public final void scaleAdd2(float s, T3 t1, T3 t2) {
+ x = s * t1.x + t2.x;
+ y = s * t1.y + t2.y;
+ z = s * t1.z + t2.z;
+ }
+
+
+ /**
+ * average of two tuples
+ *
+ * @param a
+ * @param b
+ */
+ public void ave(T3 a, T3 b) {
+ x = (a.x + b.x) / 2f;
+ y = (a.y + b.y) / 2f;
+ z = (a.z + b.z) / 2f;
+ }
+
+ /**
+ * Vector dot product. Was in Vector3f; more useful here, though.
+ *
+ * @param v
+ * the other vector
+ * @return this.dot.v
+ */
+ public final float dot(T3 v) {
+ return x * v.x + y * v.y + z * v.z;
+ }
+
+ /**
+ * Returns the squared length of this vector.
+ * Was in Vector3f; more useful here, though.
+ *
+ * @return the squared length of this vector
+ */
+ public final float lengthSquared() {
+ return x * x + y * y + z * z;
+ }
+
+ /**
+ * Returns the length of this vector.
+ * Was in Vector3f; more useful here, though.
+ *
+ * @return the length of this vector
+ */
+ public final float length() {
+ return (float) Math.sqrt(lengthSquared());
+ }
+
+ /**
+ * Normalizes this vector in place.
+ * Was in Vector3f; more useful here, though.
+ */
+ public final void normalize() {
+ double d = length();
+
+ // zero-div may occur.
+ x /= d;
+ y /= d;
+ z /= d;
+ }
+
+ /**
+ * Sets this tuple to be the vector cross product of vectors v1 and v2.
+ *
+ * @param v1
+ * the first vector
+ * @param v2
+ * the second vector
+ */
+ public final void cross(T3 v1, T3 v2) {
+ set(v1.y * v2.z - v1.z * v2.y, v1.z * v2.x - v1.x * v2.z, v1.x * v2.y
+ - v1.y * v2.x);
+ }
+
+ /**
+ * Returns a hash number based on the data values in this object. Two
+ * different Tuple3f objects with identical data values (ie, returns true for
+ * equals(Tuple3f) ) will return the same hash number. Two vectors with
+ * different data members may return the same hash value, although this is not
+ * likely.
+ */
+ @Override
+ public int hashCode() {
+ long bits = 1L;
+ bits = 31L * bits + floatToIntBits(x);
+ bits = 31L * bits + floatToIntBits(y);
+ bits = 31L * bits + floatToIntBits(z);
+ return (int) (bits ^ (bits >> 32));
+ }
+
+ static int floatToIntBits(float x) {
+ return (x == 0 ? 0 : Float.floatToIntBits(x));
+ }
+
+ /**
+ * Returns true if all of the data members of Tuple3f t1 are equal to the
+ * corresponding data members in this
+ *
+ * @param t1
+ * the vector with which the comparison is made.
+ */
+ @Override
+ public boolean equals(Object t1) {
+ if (!(t1 instanceof T3))
+ return false;
+ T3 t2 = (T3) t1;
+ return (x == t2.x && y == t2.y && z == t2.z);
+ }
+
+ /**
+ * Returns a string that contains the values of this Tuple3f. The form is
+ * (x,y,z).
+ *
+ * @return the String representation
+ */
+ @Override
+ public String toString() {
+ return "{" + x + ", " + y + ", " + z + "}";
+ }
+
+ @Override
+ public String toJSON() {
+ return "[" + x + "," + y + "," + z + "]";
+ }
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+/**
+ * A generic 3 element tuple that is represented by double precision floating
+ * point x,y and z coordinates.
+ *
+ * @version specification 1.1, implementation $Revision: 1.9 $, $Date:
+ * 2006/07/28 17:01:32 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012
+ * for unique constructor and method names
+ * for the optimization of compiled JavaScript using Java2Script.
+ *
+ */
+public abstract class T3d {
+ /**
+ * The x coordinate.
+ */
+ public double x;
+
+ /**
+ * The y coordinate.
+ */
+ public double y;
+
+ /**
+ * The z coordinate.
+ */
+ public double z;
+
+ /**
+ * Constructs and initializes a Tuple3d to (0,0,0).
+ */
+ public T3d() {
+ }
+
+ /**
+ * Sets the value of this tuple to the specified xyz coordinates.
+ *
+ * @param x
+ * the x coordinate
+ * @param y
+ * the y coordinate
+ * @param z
+ * the z coordinate
+ */
+ public final void set(double x, double y, double z) {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ }
+
+ /**
+ * Sets the value of this tuple from the 3 values specified in the array.
+ *
+ * @param t
+ * the array of length 3 containing xyz in order
+ */
+ public final void setA(double t[]) {
+ // ArrayIndexOutOfBounds is thrown if t.length < 3
+ x = t[0];
+ y = t[1];
+ z = t[2];
+ }
+
+ /**
+ * Sets the value of this tuple to the value of the Tuple3d argument.
+ *
+ * @param t1
+ * the tuple to be copied
+ */
+ public final void setT(T3d t1) {
+ x = t1.x;
+ y = t1.y;
+ z = t1.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the vector sum of tuples t1 and t2.
+ *
+ * @param t1
+ * the first tuple
+ * @param t2
+ * the second tuple
+ */
+ public final void add2(T3d t1, T3d t2) {
+ x = t1.x + t2.x;
+ y = t1.y + t2.y;
+ z = t1.z + t2.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the vector sum of itself and tuple t1.
+ *
+ * @param t1
+ * the other tuple
+ */
+ public final void add(T3d t1) {
+ x += t1.x;
+ y += t1.y;
+ z += t1.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the vector difference of tuple t1 and t2
+ * (this = t1 - t2).
+ *
+ * @param t1
+ * the first tuple
+ * @param t2
+ * the second tuple
+ */
+ public final void sub2(T3d t1, T3d t2) {
+ x = t1.x - t2.x;
+ y = t1.y - t2.y;
+ z = t1.z - t2.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the vector difference of itself and tuple
+ * t1 (this = this - t1).
+ *
+ * @param t1
+ * the other tuple
+ */
+ public final void sub(T3d t1) {
+ x -= t1.x;
+ y -= t1.y;
+ z -= t1.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the scalar multiplication of itself.
+ *
+ * @param s
+ * the scalar value
+ */
+ public final void scale(double s) {
+ x *= s;
+ y *= s;
+ z *= s;
+ }
+
+ /**
+ * Sets the value of this tuple to the scalar multiplication of tuple t1 and
+ * then adds tuple t2 (this = s*t1 + t2).
+ *
+ * @param s
+ * the scalar value
+ * @param t1
+ * the tuple to be multipled
+ * @param t2
+ * the tuple to be added
+ */
+ public final void scaleAdd(double s, T3d t1, T3d t2) {
+ x = s * t1.x + t2.x;
+ y = s * t1.y + t2.y;
+ z = s * t1.z + t2.z;
+ }
+
+ /**
+ * Returns a hash number based on the data values in this object. Two
+ * different Tuple3d objects with identical data values (ie, returns true for
+ * equals(Tuple3d) ) will return the same hash number. Two vectors with
+ * different data members may return the same hash value, although this is not
+ * likely.
+ */
+ @Override
+ public int hashCode() {
+ long xbits = doubleToLongBits0(x);
+ long ybits = doubleToLongBits0(y);
+ long zbits = doubleToLongBits0(z);
+ return (int) (xbits ^ (xbits >> 32) ^ ybits ^ (ybits >> 32) ^ zbits ^ (zbits >> 32));
+ }
+
+ static long doubleToLongBits0(double d) {
+ // Check for +0 or -0
+ return (d == 0 ? 0 : Double.doubleToLongBits(d));
+ }
+
+ /**
+ * Returns true if all of the data members of Tuple3d t1 are equal to the
+ * corresponding data members in this
+ *
+ * @param t1
+ * the vector with which the comparison is made.
+ */
+ @Override
+ public boolean equals(Object t1) {
+ if (!(t1 instanceof T3d))
+ return false;
+ T3d t2 = (T3d) t1;
+ return (this.x == t2.x && this.y == t2.y && this.z == t2.z);
+ }
+
+ /**
+ * Returns a string that contains the values of this Tuple3d. The form is
+ * (x,y,z).
+ *
+ * @return the String representation
+ */
+ @Override
+ public String toString() {
+ return "{" + x + ", " + y + ", " + z + "}";
+ }
+
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+/**
+ * A 3-element tuple represented by signed integer x,y,z coordinates.
+ *
+ * @since Java 3D 1.2
+ * @version specification 1.2, implementation $Revision: 1.9 $, $Date:
+ * 2006/07/28 17:01:32 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012 for unique
+ * constructor and method names for the optimization of compiled
+ * JavaScript using Java2Script.
+ *
+ */
+public abstract class T3i {
+
+ /**
+ * The x coordinate.
+ */
+ public int x;
+
+ /**
+ * The y coordinate.
+ */
+ public int y;
+
+ /**
+ * The z coordinate.
+ */
+ public int z;
+
+ /**
+ * Constructs and initializes a Tuple3i to (0,0,0).
+ */
+ public T3i() {
+ }
+
+ /**
+ * Sets the value of this tuple to to the specified x, y, and z coordinates.
+ *
+ * @param x
+ * the x coordinate.
+ * @param y
+ * the y coordinate.
+ * @param z
+ * the z coordinate.
+ */
+ public final void set(int x, int y, int z) {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ }
+
+ /**
+ * Sets the value of this tuple to the value of tuple t1.
+ *
+ * @param t1
+ * the tuple to be copied.
+ */
+ public final void setT(T3i t1) {
+ x = t1.x;
+ y = t1.y;
+ z = t1.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the sum of itself and t1.
+ *
+ * @param t
+ * is the other tuple
+ */
+ public final void add(T3i t) {
+ x += t.x;
+ y += t.y;
+ z += t.z;
+ }
+
+ /**
+ * Sets the value of this tuple to the scalar multiplication of tuple t1 plus
+ * tuple t2 (this = s*t1 + t2).
+ *
+ * @param s
+ * the scalar value
+ * @param t1
+ * the tuple to be multipled
+ * @param t2
+ * the tuple to be added
+ */
+ public final void scaleAdd(int s, T3i t1, T3i t2) {
+ x = s * t1.x + t2.x;
+ y = s * t1.y + t2.y;
+ z = s * t1.z + t2.z;
+ }
+
+ /**
+ * Returns a hash number based on the data values in this object. Two
+ * different Tuple3i objects with identical data values (ie, returns true for
+ * equals(Tuple3i) ) will return the same hash number. Two vectors with
+ * different data members may return the same hash value, although this is not
+ * likely.
+ */
+ @Override
+ public int hashCode() {
+ return x ^ y ^ z;
+ }
+
+ /**
+ * Returns true if the Object o is of type Tuple3i and all of the data members
+ * of t are equal to the corresponding data members in this Tuple3i.
+ *
+ * @param o
+ * the object with which the comparison is made.
+ */
+ @Override
+ public boolean equals(Object o) {
+ if (!(o instanceof T3i))
+ return false;
+ T3i t = (T3i) o;
+ return (this.x == t.x && this.y == t.y && this.z == t.z);
+ }
+
+ /**
+ * Returns a string that contains the values of this Tuple3i. The form is
+ * (x,y,z).
+ *
+ * @return the String representation
+ */
+ @Override
+ public String toString() {
+ return "(" + x + ", " + y + ", " + z + ")";
+ }
+
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+/**
+ * A generic 4 element tuple that is represented by single precision floating
+ * point x,y,z and w coordinates.
+ *
+ * @version specification 1.1, implementation $Revision: 1.9 $, $Date:
+ * 2006/07/28 17:01:32 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012
+ * for unique constructor and method names
+ * for the optimization of compiled JavaScript using Java2Script.
+ *
+ */
+public abstract class T4 extends T3 {
+
+ /**
+ * The w coordinate.
+ */
+ public float w;
+
+ /**
+ * Sets the value of this tuple to the specified xyzw coordinates.
+ *
+ * @param x
+ * the x coordinate
+ * @param y
+ * the y coordinate
+ * @param z
+ * the z coordinate
+ * @param w
+ * the w coordinate
+ */
+ public final void set4(float x, float y, float z, float w) {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ this.w = w;
+ }
+
+ /**
+ * Sets the value of this tuple to the scalar multiplication of itself.
+ *
+ * @param s
+ * the scalar value
+ */
+ public final void scale4(float s) {
+ scale(s);
+ w *= s;
+ }
+
+ /**
+ * Returns a hash number based on the data values in this object. Two
+ * different Tuple4f objects with identical data values (ie, returns true for
+ * equals(Tuple4f) ) will return the same hash number. Two vectors with
+ * different data members may return the same hash value, although this is not
+ * likely.
+ */
+ @Override
+ public int hashCode() {
+ return T3.floatToIntBits(x) ^ T3.floatToIntBits(y)
+ ^ T3.floatToIntBits(z) ^ T3.floatToIntBits(w);
+ }
+
+ /**
+ * Returns true if all of the data members of Object are equal to the
+ * corresponding data members in this
+ *
+ * @param o
+ * the vector with which the comparison is made.
+ */
+ @Override
+ public boolean equals(Object o) {
+ if (!(o instanceof T4))
+ return false;
+ T4 t = (T4) o;
+ return (this.x == t.x && this.y == t.y && this.z == t.z && this.w == t.w);
+ }
+
+ /**
+ * Returns a string that contains the values of this Tuple4f. The form is
+ * (x,y,z,w).
+ *
+ * @return the String representation
+ */
+ @Override
+ public String toString() {
+ return "(" + x + ", " + y + ", " + z + ", " + w + ")";
+ }
+
+ @Override
+ public String toJSON() {
+ return "[" + x + ", " + y + ", " + z + ", " + w + "]";
+ }
+
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+ */
+package javajs.util;
+
+
+/**
+ * A 3-element vector that is represented by single precision floating point
+ * x,y,z coordinates. If this value represents a normal, then it should be
+ * normalized.
+ *
+ * @version specification 1.1, implementation $Revision: 1.10 $, $Date:
+ * 2006/10/03 19:52:30 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012
+ * for unique constructor and method names
+ * for the optimization of compiled JavaScript using Java2Script.
+ *
+ */
+public class V3 extends T3 {
+
+ public static V3 newV(T3 t) {
+ return V3.new3(t.x, t.y, t.z);
+ }
+
+ public static V3 newVsub(T3 t1, T3 t2) {
+ return V3.new3(t1.x - t2.x, t1.y - t2.y,t1.z - t2.z);
+ }
+
+ public static V3 new3(float x, float y, float z) {
+ V3 v = new V3();
+ v.x = x;
+ v.y = y;
+ v.z = z;
+ return v;
+ }
+
+ /**
+ * Returns the angle in radians between this vector and the vector parameter;
+ * the return value is constrained to the range [0,PI].
+ *
+ * @param v1
+ * the other vector
+ * @return the angle in radians in the range [0,PI]
+ */
+ public final float angle(V3 v1) {
+ // return (double)Math.acos(dot(v1)/v1.length()/v.length());
+ // Numerically, near 0 and PI are very bad condition for acos.
+ // In 3-space, |atan2(sin,cos)| is much stable.
+
+ double xx = y * v1.z - z * v1.y;
+ double yy = z * v1.x - x * v1.z;
+ double zz = x * v1.y - y * v1.x;
+ double cross = Math.sqrt(xx * xx + yy * yy + zz * zz);
+
+ return (float) Math.abs(Math.atan2(cross, dot(v1)));
+ }
+}
--- /dev/null
+/*
+ Copyright (C) 1997,1998,1999
+ Kenji Hiranabe, Eiwa System Management, Inc.
+
+ This program is free software.
+ Implemented by Kenji Hiranabe(hiranabe@esm.co.jp),
+ conforming to the Java(TM) 3D API specification by Sun Microsystems.
+
+ Permission to use, copy, modify, distribute and sell this software
+ and its documentation for any purpose is hereby granted without fee,
+ provided that the above copyright notice appear in all copies and
+ that both that copyright notice and this permission notice appear
+ in supporting documentation. Kenji Hiranabe and Eiwa System Management,Inc.
+ makes no representations about the suitability of this software for any
+ purpose. It is provided "AS IS" with NO WARRANTY.
+*/
+package javajs.util;
+
+
+
+
+/**
+ * A 3 element vector that is represented by double precision floating point
+ * x,y,z coordinates. If this value represents a normal, then it should be
+ * normalized.
+ *
+ * @version specification 1.1, implementation $Revision: 1.9 $, $Date:
+ * 2006/07/28 17:01:32 $
+ * @author Kenji hiranabe
+ *
+ * additions by Bob Hanson hansonr@stolaf.edu 9/30/2012
+ * for unique constructor and method names
+ * for the optimization of compiled JavaScript using Java2Script.
+ *
+ */
+public class V3d extends T3d {
+
+ /**
+ * Sets this vector to be the vector cross product of vectors v1 and v2.
+ *
+ * @param v1
+ * the first vector
+ * @param v2
+ * the second vector
+ */
+ public final void cross(V3d v1, V3d v2) {
+ // store on stack once for aliasing-safty
+ // i.e. safe when a.cross(a, b)
+ set(v1.y * v2.z - v1.z * v2.y, v1.z * v2.x - v1.x * v2.z, v1.x * v2.y
+ - v1.y * v2.x);
+ }
+
+ /**
+ * Normalizes this vector in place.
+ */
+ public final void normalize() {
+ double d = length();
+
+ // zero-div may occur.
+ x /= d;
+ y /= d;
+ z /= d;
+ }
+
+ /**
+ * Computes the dot product of the this vector and vector v.
+ *
+ * @param v
+ * the other vector
+ * @return this.dot.v
+ */
+ public final double dot(V3d v) {
+ return x * v.x + y * v.y + z * v.z;
+ }
+
+ /**
+ * Returns the squared length of this vector.
+ *
+ * @return the squared length of this vector
+ */
+ public final double lengthSquared() {
+ return x * x + y * y + z * z;
+ }
+
+ /**
+ * Returns the length of this vector.
+ *
+ * @return the length of this vector
+ */
+ public final double length() {
+ return Math.sqrt(lengthSquared());
+ }
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2006 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package javajs.util;
+
+/**
+ * A very simplistic XML generator
+ */
+
+public class XmlUtil {
+
+ public XmlUtil() {
+ // Jmol's PropertyManager and JvxlCoder classes use reflection
+ }
+ public static void openDocument(SB data) {
+ data.append("<?xml version=\"1.0\"?>\n");
+ }
+
+ public static void openTag(SB sb, String name) {
+ sb.append("<").append(name).append(">\n");
+ }
+
+ public static void openTagAttr(SB sb, String name, Object[] attributes) {
+ appendTagAll(sb, name, attributes, null, false, false);
+ sb.append("\n");
+ }
+
+ public static void closeTag(SB sb, String name) {
+ sb.append("</").append(name).append(">\n");
+ }
+
+ public static void appendTagAll(SB sb, String name,
+ Object[] attributes, Object data,
+ boolean isCdata, boolean doClose) {
+ String closer = ">";
+ if (name.endsWith("/")){
+ name = name.substring(0, name.length() - 1);
+ if (data == null) {
+ closer = "/>\n";
+ doClose = false;
+ }
+ }
+ sb.append("<").append(name);
+ if (attributes != null)
+ for (int i = 0; i < attributes.length; i++) {
+ Object o = attributes[i];
+ if (o == null)
+ continue;
+ if (o instanceof Object[])
+ for (int j = 0; j < ((Object[]) o).length; j+= 2)
+ appendAttrib(sb, ((Object[]) o)[j], ((Object[]) o)[j + 1]);
+ else
+ appendAttrib(sb, o, attributes[++i]);
+ }
+ sb.append(closer);
+ if (data != null) {
+ if (isCdata)
+ data = wrapCdata(data);
+ sb.appendO(data);
+ }
+ if (doClose)
+ closeTag(sb, name);
+ }
+
+ /**
+ * wrap the string as character data, with replacements for [ noted
+ * as a list starting with * after the CDATA termination
+ *
+ * @param data
+ * @return wrapped text
+ */
+ public static String wrapCdata(Object data) {
+ String s = "" + data;
+ return (s.indexOf("&") < 0 && s.indexOf("<") < 0 ? (s.startsWith("\n") ? "" : "\n") + s
+ : "<![CDATA[" + PT.rep(s, "]]>", "]]]]><![CDATA[>") + "]]>");
+ }
+
+ /**
+ * standard <name attr="..." attr="...">data</name>"
+ *
+ * @param sb
+ * @param name
+ * @param attributes
+ * @param data
+ */
+ public static void appendTagObj(SB sb, String name,
+ Object[] attributes, Object data) {
+ appendTagAll(sb, name, attributes, data, false, true);
+ }
+
+ /**
+ * standard <name>data</name>"
+ * standard <name attr="..." attr="..."></name>"
+ *
+ * @param sb
+ * @param name
+ * @param data
+ */
+ public static void appendTag(SB sb, String name, Object data) {
+ if (data instanceof Object[])
+ appendTagAll(sb, name, (Object[]) data, null, false, true);
+ else
+ appendTagAll(sb, name, null, data, false, true);
+ }
+
+ /**
+ * <name><![CDATA[data]]></name>"
+ *
+ * will convert ]]> to ]] >
+ *
+ * @param sb
+ * @param name
+ * @param attributes
+ * @param data
+ */
+ public static void appendCdata(SB sb, String name,
+ Object[] attributes, String data) {
+ appendTagAll(sb, name, attributes, data, true, true);
+ }
+
+ /**
+ *
+ * @param sb
+ * @param name
+ * @param value
+ */
+ public static void appendAttrib(SB sb, Object name, Object value) {
+ if (value == null)
+ return;
+
+ // note: <&" are disallowed but not checked for here
+
+ sb.append(" ").appendO(name).append("=\"").appendO(value).append("\"");
+ }
+
+// /**
+// * @param s
+// * @return unwrapped text
+// */
+// public static String unwrapCdata(String s) {
+// return (s.startsWith("<![CDATA[") && s.endsWith("]]>") ?
+// PT.rep(s.substring(9, s.length()-3),"]]]]><![CDATA[>", "]]>") : s);
+// }
+//
+
+}
--- /dev/null
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2006 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package javajs.util;
+
+import java.io.BufferedInputStream;
+
+import javajs.api.GenericZipTools;
+
+
+
+
+public class ZipData {
+ boolean isEnabled = true;
+ byte[] buf;
+ int pt;
+ int nBytes;
+
+ public ZipData(int nBytes) {
+ this.nBytes = nBytes;
+ }
+
+ public int addBytes(byte[] byteBuf, int nSectorBytes, int nBytesRemaining) {
+ if (pt == 0) {
+ if (!Rdr.isGzipB(byteBuf)) {
+ isEnabled = false;
+ return -1;
+ }
+ buf = new byte[nBytesRemaining];
+ }
+ int nToAdd = Math.min(nSectorBytes, nBytesRemaining);
+ System.arraycopy(byteBuf, 0, buf, pt, nToAdd);
+ pt += nToAdd;
+ return nBytesRemaining - nToAdd;
+ }
+
+ public void addTo(GenericZipTools jzt, SB data) {
+ data.append(getGzippedBytesAsString(jzt, buf));
+ }
+
+ static String getGzippedBytesAsString(GenericZipTools jzt, byte[] bytes) {
+ try {
+ BufferedInputStream bis = jzt.getUnGzippedInputStream(bytes);
+ String s = ZipTools.getStreamAsString(bis);
+ bis.close();
+ return s;
+ } catch (Exception e) {
+ return "";
+ }
+ }
+
+
+}
+
--- /dev/null
+/* $RCSfile$
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2006 The Jmol Development Team
+ *
+ * Contact: jmol-developers@lists.sf.net
+ *
+ * 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 Public 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 Street, Fifth Floor, Boston, MA
+ * 02110-1301, USA.
+ */
+
+package javajs.util;
+
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+import javajs.J2SIgnoreImport;
+import javajs.api.GenericZipInputStream;
+import javajs.api.GenericZipTools;
+import javajs.api.ZInputStream;
+
+import java.util.Map;
+import java.util.zip.CRC32;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+import java.util.zip.ZipOutputStream;
+
+
+/**
+ * Note the JSmol/HTML5 must use its own version of java.util.zip.ZipOutputStream.
+ *
+ */
+@J2SIgnoreImport({ java.util.zip.ZipOutputStream.class })
+public class ZipTools implements GenericZipTools {
+
+ public ZipTools() {
+ // for reflection
+ }
+
+ @Override
+ public ZInputStream newZipInputStream(InputStream is) {
+ return newZIS(is);
+ }
+
+ private static ZInputStream newZIS(InputStream is) {
+ return (is instanceof ZInputStream ? (ZInputStream) is
+ : is instanceof BufferedInputStream ? new GenericZipInputStream(is)
+ : new GenericZipInputStream(new BufferedInputStream(is)));
+ }
+
+ /**
+ * reads a ZIP file and saves all data in a Hashtable so that the files may be
+ * organized later in a different order. Also adds a #Directory_Listing entry.
+ *
+ * Files are bracketed by BEGIN Directory Entry and END Directory Entry lines,
+ * similar to CompoundDocument.getAllData.
+ *
+ * @param is
+ * @param subfileList
+ * @param name0
+ * prefix for entry listing
+ * @param binaryFileList
+ * |-separated list of files that should be saved as xx xx xx hex byte
+ * strings. The directory listing is appended with ":asBinaryString"
+ * @param fileData
+ */
+ @Override
+ public void getAllZipData(InputStream is, String[] subfileList,
+ String name0, String binaryFileList, String exclude,
+ Map<String, String> fileData) {
+ ZipInputStream zis = (ZipInputStream) newZIS(is);
+ ZipEntry ze;
+ SB listing = new SB();
+ binaryFileList = "|" + binaryFileList + "|";
+ String prefix = PT.join(subfileList, '/', 1);
+ String prefixd = null;
+ if (prefix != null) {
+ prefixd = prefix.substring(0, prefix.indexOf("/") + 1);
+ if (prefixd.length() == 0)
+ prefixd = null;
+ }
+ try {
+ while ((ze = zis.getNextEntry()) != null) {
+ String name = ze.getName();
+ if (prefix != null && prefixd != null
+ && !(name.equals(prefix) || name.startsWith(prefixd))
+ || exclude != null && name.contains(exclude))
+ continue;
+ //System.out.println("ziputil: " + name);
+ listing.append(name).appendC('\n');
+ String sname = "|" + name.substring(name.lastIndexOf("/") + 1) + "|";
+ boolean asBinaryString = (binaryFileList.indexOf(sname) >= 0);
+ byte[] bytes = Rdr.getLimitedStreamBytes(zis, ze.getSize());
+ String str;
+ if (asBinaryString) {
+ str = getBinaryStringForBytes(bytes);
+ name += ":asBinaryString";
+ } else {
+ str = Rdr.fixUTF(bytes);
+ }
+ str = "BEGIN Directory Entry " + name + "\n" + str
+ + "\nEND Directory Entry " + name + "\n";
+ String key = name0 + "|" + name;
+ fileData.put(key, str);
+ }
+ } catch (Exception e) {
+ }
+ fileData.put("#Directory_Listing", listing.toString());
+ }
+
+ private String getBinaryStringForBytes(byte[] bytes) {
+ SB ret = new SB();
+ for (int i = 0; i < bytes.length; i++)
+ ret.append(Integer.toHexString(bytes[i] & 0xFF)).appendC(' ');
+ return ret.toString();
+ }
+
+ /**
+ * iteratively drills into zip files of zip files to extract file content or
+ * zip file directory. Also works with JAR files.
+ *
+ * Does not return "__MACOS" paths
+ *
+ * @param bis
+ * @param list
+ * @param listPtr
+ * @param asBufferedInputStream
+ * for Pmesh
+ * @return directory listing or subfile contents
+ */
+ @Override
+ public Object getZipFileDirectory(BufferedInputStream bis, String[] list,
+ int listPtr, boolean asBufferedInputStream) {
+ SB ret;
+ if (list == null || listPtr >= list.length)
+ return getZipDirectoryAsStringAndClose(bis);
+ bis = Rdr.getPngZipStream(bis, true);
+ String fileName = list[listPtr];
+ ZipInputStream zis = new ZipInputStream(bis);
+ ZipEntry ze;
+ //System.out.println("fname=" + fileName);
+ try {
+ boolean isAll = (fileName.equals("."));
+ if (isAll || fileName.lastIndexOf("/") == fileName.length() - 1) {
+ ret = new SB();
+ while ((ze = zis.getNextEntry()) != null) {
+ String name = ze.getName();
+ if (isAll || name.startsWith(fileName))
+ ret.append(name).appendC('\n');
+ }
+ String str = ret.toString();
+ return (asBufferedInputStream ? Rdr.getBIS(str.getBytes()) : str);
+ }
+ int pt = fileName.indexOf(":asBinaryString");
+ boolean asBinaryString = (pt > 0);
+ if (asBinaryString)
+ fileName = fileName.substring(0, pt);
+ fileName = fileName.replace('\\', '/');
+ while ((ze = zis.getNextEntry()) != null
+ && !fileName.equals(ze.getName())) {
+ }
+ byte[] bytes = (ze == null ? null : Rdr.getLimitedStreamBytes(zis,
+ ze.getSize()));
+ ze = null;
+ zis.close();
+ if (bytes == null)
+ return "";
+ if (Rdr.isZipB(bytes) || Rdr.isPngZipB(bytes))
+ return getZipFileDirectory(Rdr.getBIS(bytes), list, ++listPtr,
+ asBufferedInputStream);
+ if (asBufferedInputStream)
+ return Rdr.getBIS(bytes);
+ if (asBinaryString) {
+ ret = new SB();
+ for (int i = 0; i < bytes.length; i++)
+ ret.append(Integer.toHexString(bytes[i] & 0xFF)).appendC(' ');
+ return ret.toString();
+ }
+ if (Rdr.isGzipB(bytes))
+ bytes = Rdr.getLimitedStreamBytes(getUnGzippedInputStream(bytes), -1);
+ return Rdr.fixUTF(bytes);
+ } catch (Exception e) {
+ return "";
+ }
+ }
+
+ @Override
+ public byte[] getZipFileContentsAsBytes(BufferedInputStream bis,
+ String[] list, int listPtr) {
+ byte[] ret = new byte[0];
+ String fileName = list[listPtr];
+ if (fileName.lastIndexOf("/") == fileName.length() - 1)
+ return ret;
+ try {
+ bis = Rdr.getPngZipStream(bis, true);
+ ZipInputStream zis = new ZipInputStream(bis);
+ ZipEntry ze;
+ while ((ze = zis.getNextEntry()) != null) {
+ if (!fileName.equals(ze.getName()))
+ continue;
+ byte[] bytes = Rdr.getLimitedStreamBytes(zis, ze.getSize());
+ return ((Rdr.isZipB(bytes) || Rdr.isPngZipB(bytes)) && ++listPtr < list.length ? getZipFileContentsAsBytes(
+ Rdr.getBIS(bytes), list, listPtr) : bytes);
+ }
+ } catch (Exception e) {
+ }
+ return ret;
+ }
+
+ @Override
+ public String getZipDirectoryAsStringAndClose(BufferedInputStream bis) {
+ SB sb = new SB();
+ String[] s = new String[0];
+ try {
+ s = getZipDirectoryOrErrorAndClose(bis, null);
+ bis.close();
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ }
+ for (int i = 0; i < s.length; i++)
+ sb.append(s[i]).appendC('\n');
+ return sb.toString();
+ }
+
+ @Override
+ public String[] getZipDirectoryAndClose(BufferedInputStream bis,
+ String manifestID) {
+ String[] s = new String[0];
+ try {
+ s = getZipDirectoryOrErrorAndClose(bis, manifestID);
+ bis.close();
+ } catch (Exception e) {
+ System.out.println(e.toString());
+ }
+ return s;
+ }
+
+ private String[] getZipDirectoryOrErrorAndClose(BufferedInputStream bis,
+ String manifestID)
+ throws IOException {
+ bis = Rdr.getPngZipStream(bis, true);
+ Lst<String> v = new Lst<String>();
+ ZipInputStream zis = new ZipInputStream(bis);
+ ZipEntry ze;
+ String manifest = null;
+ while ((ze = zis.getNextEntry()) != null) {
+ String fileName = ze.getName();
+ if (manifestID != null && fileName.startsWith(manifestID))
+ manifest = getStreamAsString(zis);
+ else if (!fileName.startsWith("__MACOS")) // resource fork not nec.
+ v.addLast(fileName);
+ }
+ zis.close();
+ if (manifestID != null)
+ v.add(0, manifest == null ? "" : manifest + "\n############\n");
+ return v.toArray(new String[v.size()]);
+ }
+
+ public static String getStreamAsString(InputStream is) throws IOException {
+ return Rdr.fixUTF(Rdr.getLimitedStreamBytes(is, -1));
+ }
+
+ @Override
+ public InputStream newGZIPInputStream(InputStream is) throws IOException {
+ return new BufferedInputStream(new GZIPInputStream(is, 512));
+ }
+
+ @Override
+ public BufferedInputStream getUnGzippedInputStream(byte[] bytes) {
+ try {
+ return Rdr.getUnzippedInputStream(this, Rdr.getBIS(bytes));
+ } catch (Exception e) {
+ return null;
+ }
+ }
+
+ @Override
+ public void addZipEntry(Object zos, String fileName) throws IOException {
+ ((ZipOutputStream) zos).putNextEntry(new ZipEntry(fileName));
+ }
+
+ @Override
+ public void closeZipEntry(Object zos) throws IOException {
+ ((ZipOutputStream) zos).closeEntry();
+ }
+
+ @Override
+ public Object getZipOutputStream(Object bos) {
+ /**
+ * @j2sNative
+ *
+ * return javajs.api.Interface.getInterface(
+ * "java.util.zip.ZipOutputStream").setZOS(bos);
+ *
+ */
+ {
+ return new ZipOutputStream((OutputStream) bos);
+ }
+ }
+
+ @Override
+ public int getCrcValue(byte[] bytes) {
+ CRC32 crc = new CRC32();
+ crc.update(bytes, 0, bytes.length);
+ return (int) crc.getValue();
+ }
+
+ @Override
+ public void readFileAsMap(BufferedInputStream bis, Map<String, Object> bdata, String name) {
+ readFileAsMapStatic(bis, bdata, name);
+ }
+
+ public static void readFileAsMapStatic(BufferedInputStream bis,
+ Map<String, Object> bdata, String name) {
+ int pt = (name == null ? -1 : name.indexOf("|"));
+ name = (pt >= 0 ? name.substring(pt + 1) : null);
+ try {
+ if (Rdr.isPngZipStream(bis)) {
+ boolean isImage = "_IMAGE_".equals(name);
+ if (name == null || isImage)
+ bdata.put((isImage ? "_DATA_" : "_IMAGE_"), new BArray(getPngImageBytes(bis)));
+ if (!isImage)
+ cacheZipContentsStatic(bis, name, bdata, true);
+ } else if (Rdr.isZipS(bis)) {
+ cacheZipContentsStatic(bis, name, bdata, true);
+ } else if (name == null){
+ bdata.put("_DATA_", new BArray(Rdr.getLimitedStreamBytes(bis, -1)));
+ } else {
+ throw new IOException("ZIP file " + name + " not found");
+ }
+ bdata.put("$_BINARY_$", Boolean.TRUE);
+ } catch (IOException e) {
+ bdata.clear();
+ bdata.put("_ERROR_", e.getMessage());
+ }
+ }
+
+ @Override
+ public String cacheZipContents(BufferedInputStream bis,
+ String fileName,
+ Map<String, Object> cache,
+ boolean asByteArray) {
+ return cacheZipContentsStatic(bis, fileName, cache, asByteArray);
+ }
+
+ /**
+ *
+ * @param bis
+ * @param fileName may end with "/" for a prefix or contain "|xxxx.xxx" for a specific file or be null
+ * @param cache
+ * @param asByteArray
+ * @return
+ */
+ public static String cacheZipContentsStatic(BufferedInputStream bis,
+ String fileName, Map<String, Object> cache, boolean asByteArray) {
+ ZipInputStream zis = (ZipInputStream) newZIS(bis);
+ ZipEntry ze;
+ SB listing = new SB();
+ long n = 0;
+ boolean isPath = (fileName != null && fileName.endsWith("/"));
+ boolean oneFile = (asByteArray && !isPath && fileName != null);
+ int pt = (oneFile ? fileName.indexOf("|") : -1);
+ String file0 = (pt >= 0 ? fileName : null);
+ if (pt >= 0)
+ fileName = fileName.substring(0, pt);
+ String prefix = (fileName == null ? "" : isPath ? fileName : fileName + "|");
+ try {
+ while ((ze = zis.getNextEntry()) != null) {
+ String name = ze.getName();
+ if (fileName != null) {
+ if (oneFile) {
+ if (!name.equalsIgnoreCase(fileName))
+ continue;
+ } else {
+ listing.append(name).appendC('\n');
+ }
+ }
+ long nBytes = ze.getSize();
+ byte[] bytes = Rdr.getLimitedStreamBytes(zis, nBytes);
+ if (file0 != null) {
+ readFileAsMapStatic(Rdr.getBIS(bytes), cache, file0);
+ return null;
+ }
+ n += bytes.length;
+ Object o = (asByteArray ? new BArray(bytes) : bytes);
+ cache.put((oneFile ? "_DATA_" : prefix + name), o);
+ if (oneFile)
+ break;
+ }
+ zis.close();
+ } catch (Exception e) {
+ try {
+ zis.close();
+ } catch (IOException e1) {
+ }
+ return null;
+ }
+ if (n == 0 || fileName == null)
+ return null;
+ System.out.println("ZipTools cached " + n + " bytes from " + fileName);
+ return listing.toString();
+ }
+
+ private static byte[] getPngImageBytes(BufferedInputStream bis) {
+ try {
+ if (Rdr.isPngZipStream(bis)) {
+ int pt_count[] = new int[2];
+ Rdr.getPngZipPointAndCount(bis, pt_count);
+ if (pt_count[1] != 0)
+ return deActivatePngZipB(Rdr.getLimitedStreamBytes(bis, pt_count[0]));
+ }
+ return Rdr.getLimitedStreamBytes(bis, -1);
+ } catch (IOException e) {
+ return null;
+ }
+ }
+
+ /**
+ * Once a PNGJ image has been extracted, we want to red-line its
+ * iTXt "Jmol Type PNGJ" tag, since it is no longer associated with
+ * ZIP data.
+ *
+ * @param bytes
+ * @return disfigured bytes
+ *
+ */
+ private static byte[] deActivatePngZipB(byte[] bytes) {
+ // \0PNGJ starting at byte 50 changed to \0 NGJ
+ if (Rdr.isPngZipB(bytes))
+ bytes[51] = 32;
+ return bytes;
+ }
+
+
+
+}
git://source.jalview.org / jalview.git / commitdiff