+++ /dev/null
-/**
- *
- */
-package org.vamsas.objects.utils;
-import java.util.Vector;
-
-
-import uk.ac.vamsas.client.ClientHandle;
-import uk.ac.vamsas.client.UserHandle;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasArchiveReader;
-import uk.ac.vamsas.objects.core.*;
-/**
- * Form, accessors and validation for ApplicationData references in
- * vamsas document.
- * TODO: LATER:extend XML Schema to properly validate against the same forms required by this class
- * TODO: VAMSAS: URNS for appDatas are supposed to be unique, aren't they ?
- */
-public class AppDataReference {
- /**
- * search interface for collecting particular types of AppDatas in a vamsas document
- * @author jimp
- *
- */
- interface IAppDSearch {
- /**
- * process the appData Vobject d
- * @param d
- * @return true if appData should be collected
- */
- public boolean process(AppData d);
- }
- /**
- * collect all appData reference strings in a vamsas document
- * @param doc
- * @return vector of String objects
- */
- static public Vector getAppDataReferences(VamsasDocument doc) {
- if ((doc!=null) && (doc.getApplicationDataCount()>0)) {
- Vector apdrefs = new Vector();
- ApplicationData[] appdatas = doc.getApplicationData();
- for (int q=0; q<appdatas.length; q++) {
- String refstring=appdatas[q].getDataReference();
- if (refstring!=null)
- apdrefs.add(refstring);
- User users[] = appdatas[q].getUser();
-
- if (users!=null)
- for (int u=0; u<users.length; u++) {
- refstring=users[u].getDataReference();
- if (refstring!=null)
- apdrefs.add(new String(refstring)); // avoid referencing.
- }
- }
- if (apdrefs.size()>0)
- return apdrefs;
- }
- return null;
- }
- /**
- * General search through the set of AppData objects for a particular profile of Client and User handle.
- * @param doc
- * @param test interface implemented by the filter selecting particular AppDatas.
- * @param cascade if true only User objects for ApplicationData objects that test.process returned true will be tested.
- * @return set of uk.ac.vamsas.objects.core.AppData objects for which test.process returned true
- */
- static public Vector searchAppDatas(VamsasDocument doc, IAppDSearch test, boolean cascade) {
- if ((doc!=null) && (doc.getApplicationDataCount()>0)) {
- Vector apdrefs = new Vector();
- ApplicationData[] appdatas = doc.getApplicationData();
- for (int q=0; q<appdatas.length; q++) {
- boolean t;
- if (t=test.process(appdatas[q]))
- apdrefs.add(appdatas[q]);
- if (t || cascade) {
- User users[] = appdatas[q].getUser();
- if (users!=null)
- for (int u=0; u<users.length; u++)
- if (test.process(users[u]))
- apdrefs.add(users[u]);
- }
- }
- if (apdrefs.size()>0)
- return apdrefs;
- }
- return null;
- }
- static public boolean equals(User p, UserHandle u) {
- if (p.getFullname().equals(u.getFullName())
- && p.getOrganization().equals(u.getOrganization()))
- return true;
- return false;
- }
- /**
- * returns true if Name matches in c and p, and Urn's match (or c.getUrn()==null) and Version's match (or c.getVersion()==null)
- * @param p
- * @param c
- * @return match of p on template c.
- */
- static public boolean equals(ApplicationData p, ClientHandle c) {
- if (
- //((c.getClientUrn()==null) || p.getUrn().equals(c.getClientUrn()))
- //&&
- (p.getName().equals(c.getClientName()))
- &&
- ((c.getVersion()==null) || (p.getVersion().equals(c.getVersion())))
- )
- return true;
- return false;
- }
- /**
- * Searches document appData structure for particular combinations of client and user data
- * @param doc the data
- * @param user template user data to match against
- * @see AppDataReference.equals(uk.ac.vamsas.objects.core.User, uk.ac.vamsas.client.UserHandle)
- * @param app
- * @see AppDataReference.equals(uk.ac.vamsas.objects.core.ApplicationData, uk.ac.vamsas.client.ClientHandle)
- * @return set of matching client app datas for this client and user combination
- */
- static public Vector getUserandApplicationsData(VamsasDocument doc, UserHandle user, ClientHandle app) {
- if (doc==null) {
- return null;
- }
- final UserHandle u = user;
- final ClientHandle c = app;
-
- IAppDSearch match = new IAppDSearch() {
- public boolean process(AppData p) {
- if (p instanceof User) {
- if (AppDataReference.equals((User) p, u))
- return true;
- } else
- if (p instanceof ApplicationData) {
- if (AppDataReference.equals((ApplicationData) p, c))
- return true;
- }
- return false;
- }
- };
-
- return searchAppDatas(doc, match, true); // only return AppDatas belonging to appdata app.
- }
- /**
- * safely creates a new appData reference
- * @param dest destination document Vobject
- * @param entry base application reference to make unique
- */
- public static String uniqueAppDataReference(VamsasDocument dest,String base) {
- String urn = new String(base);
-
- for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
- ApplicationData o = dest.getApplicationData()[i];
- // ensure new urn is really unique
- int v = 1;
- // TODO: while (o.getUrn().equals(urn)) {
- urn = base+"/"+v++;
- //}
- }
- return urn;
- }
-}
+++ /dev/null
-package org.vamsas.objects.utils;
-
-import org.vamsas.objects.utils.document.VersionEntries;
-
-import uk.ac.vamsas.objects.core.*;
-
-/**
- * various vamsas-client independent helpers
- * for creating and manipulating the vamsasDocument Vobject
- * @author jimp
- *
- */
-public class DocumentStuff {
- public static VamsasDocument newVamsasDocument(VAMSAS root[], String version) {
- return newVamsasDocument(root, ProvenanceStuff.newProvenance(
- "AUTO:org.vamsas.DocumentStuff.newVamsasDocument",
- "Vamsas Document created"),
- version);
- }
- public static VamsasDocument newVamsasDocument(VAMSAS root[]) {
- return newVamsasDocument(root, ProvenanceStuff.newProvenance(
- "AUTO:org.vamsas.DocumentStuff.newVamsasDocument",
- "Vamsas Document created"),
- VersionEntries.latestVersion());
- }
- public static VamsasDocument newVamsasDocument(VAMSAS root[], Provenance p, String version) {
- VamsasDocument doc = new VamsasDocument();
- for (int r=0; r<root.length; r++) {
- doc.addVAMSAS(root[r]);
- }
- doc.setProvenance(p);
- doc.setVersion(version);
- return doc;
- }
-}
+++ /dev/null
-/*\r
- * Cay S. Horstmann & Gary Cornell, Core Java\r
- * Published By Sun Microsystems Press/Prentice-Hall\r
- * Copyright (C) 1997 Sun Microsystems Inc.\r
- * All Rights Reserved.\r
- *\r
- * Permission to use, copy, modify, and distribute this \r
- * software and its documentation for NON-COMMERCIAL purposes\r
- * and without fee is hereby granted provided that this \r
- * copyright notice appears in all copies. \r
- * \r
- * THE AUTHORS AND PUBLISHER MAKE NO REPRESENTATIONS OR \r
- * WARRANTIES ABOUT THE SUITABILITY OF THE SOFTWARE, EITHER \r
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE \r
- * IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A \r
- * PARTICULAR PURPOSE, OR NON-INFRINGEMENT. THE AUTHORS\r
- * AND PUBLISHER SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED \r
- * BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING \r
- * THIS SOFTWARE OR ITS DERIVATIVES.\r
- */\r
-\r
-/**\r
- * A class for formatting numbers that follows printf conventions.\r
- * Also implements C-like atoi and atof functions\r
- * @version 1.03 25 Oct 1997\r
- * @author Cay Horstmann\r
- */\r
-\r
-package org.vamsas.objects.utils;\r
-\r
-import java.io.*;\r
-\r
-public class Format { /**\r
- * Formats the number following printf conventions.\r
- * Main limitation: Can only handle one format parameter at a time\r
- * Use multiple Format objects to format more than one number\r
- * @param s the format string following printf conventions\r
- * The string has a prefix, a format code and a suffix. The prefix and suffix\r
- * become part of the formatted output. The format code directs the\r
- * formatting of the (single) parameter to be formatted. The code has the\r
- * following structure\r
- * <ul>\r
- * <li> a % (required)\r
- * <li> a modifier (optional)\r
- * <dl>\r
- * <dt> + <dd> forces display of + for positive numbers\r
- * <dt> 0 <dd> show leading zeroes\r
- * <dt> - <dd> align left in the field\r
- * <dt> space <dd> prepend a space in front of positive numbers\r
- * <dt> # <dd> use "alternate" format. Add 0 or 0x for octal or hexadecimal numbers. Don't suppress trailing zeroes in general floating point format.\r
- * </dl>\r
- * <li> an integer denoting field width (optional)\r
- * <li> a period followed by an integer denoting precision (optional)\r
- * <li> a format descriptor (required)\r
- * <dl>\r
- * <dt>f <dd> floating point number in fixed format\r
- * <dt>e, E <dd> floating point number in exponential notation (scientific format). The E format results in an uppercase E for the exponent (1.14130E+003), the e format in a lowercase e.\r
- * <dt>g, G <dd> floating point number in general format (fixed format for small numbers, exponential format for large numbers). Trailing zeroes are suppressed. The G format results in an uppercase E for the exponent (if any), the g format in a lowercase e.\r
- * <dt>d, i <dd> integer in decimal\r
- * <dt>x <dd> integer in hexadecimal\r
- * <dt>o <dd> integer in octal\r
- * <dt>s <dd> string\r
- * <dt>c <dd> character\r
- * </dl>\r
- * </ul>\r
- * @exception IllegalArgumentException if bad format\r
- */\r
-\r
- public Format(String s) {\r
- width = 0;\r
- precision = -1;\r
- pre = "";\r
- post = "";\r
- leading_zeroes = false;\r
- show_plus = false;\r
- alternate = false;\r
- show_space = false;\r
- left_align = false;\r
- fmt = ' ';\r
-\r
- int state = 0;\r
- int length = s.length();\r
- int parse_state = 0;\r
- // 0 = prefix, 1 = flags, 2 = width, 3 = precision,\r
- // 4 = format, 5 = end\r
- int i = 0;\r
-\r
- while (parse_state == 0) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if (s.charAt(i) == '%') {\r
- if (i < length - 1) {\r
- if (s.charAt(i + 1) == '%') {\r
- pre = pre + '%';\r
- i++;\r
- } else\r
- parse_state = 1;\r
- } else\r
- throw new java.lang.IllegalArgumentException();\r
- } else\r
- pre = pre + s.charAt(i);\r
- i++;\r
- }\r
- while (parse_state == 1) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if (s.charAt(i) == ' ')\r
- show_space = true;\r
- else if (s.charAt(i) == '-')\r
- left_align = true;\r
- else if (s.charAt(i) == '+')\r
- show_plus = true;\r
- else if (s.charAt(i) == '0')\r
- leading_zeroes = true;\r
- else if (s.charAt(i) == '#')\r
- alternate = true;\r
- else {\r
- parse_state = 2;\r
- i--;\r
- }\r
- i++;\r
- }\r
- while (parse_state == 2) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') {\r
- width = width * 10 + s.charAt(i) - '0';\r
- i++;\r
- } else if (s.charAt(i) == '.') {\r
- parse_state = 3;\r
- precision = 0;\r
- i++;\r
- } else\r
- parse_state = 4;\r
- }\r
- while (parse_state == 3) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') {\r
- precision = precision * 10 + s.charAt(i) - '0';\r
- i++;\r
- } else\r
- parse_state = 4;\r
- }\r
- if (parse_state == 4) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else\r
- fmt = s.charAt(i);\r
- i++;\r
- }\r
- if (i < length)\r
- post = s.substring(i, length);\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the double to print\r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, double x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the long to print\r
- */\r
- public static void print(java.io.PrintStream s, String fmt, long x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the character to \r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, char x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream, fmt the format string\r
- * @param x a string that represents the digits to print\r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, String x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * Converts a string of digits (decimal, octal or hex) to an integer\r
- * @param s a string\r
- * @return the numeric value of the prefix of s representing a base 10 integer\r
- */\r
-\r
- public static int atoi(String s) {\r
- return (int)atol(s);\r
- }\r
-\r
- /**\r
- * Converts a string of digits (decimal, octal or hex) to a long integer\r
- * @param s a string\r
- * @return the numeric value of the prefix of s representing a base 10 integer\r
- */\r
-\r
- public static long atol(String s) {\r
- int i = 0;\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '0') {\r
- if (i + 1 < s.length() && (s.charAt(i + 1) == 'x' || s.charAt(i + 1) == 'X'))\r
- return parseLong(s.substring(i + 2), 16);\r
- else\r
- return parseLong(s, 8);\r
- } else\r
- return parseLong(s, 10);\r
- }\r
-\r
- private static long parseLong(String s, int base) {\r
- int i = 0;\r
- int sign = 1;\r
- long r = 0;\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '-') {\r
- sign = -1;\r
- i++;\r
- } else if (i < s.length() && s.charAt(i) == '+') {\r
- i++;\r
- }\r
- while (i < s.length()) {\r
- char ch = s.charAt(i);\r
- if ('0' <= ch && ch < '0' + base)\r
- r = r * base + ch - '0';\r
- else if ('A' <= ch && ch < 'A' + base - 10)\r
- r = r * base + ch - 'A' + 10 ;\r
- else if ('a' <= ch && ch < 'a' + base - 10)\r
- r = r * base + ch - 'a' + 10 ;\r
- else\r
- return r * sign;\r
- i++;\r
- }\r
- return r * sign;\r
- }\r
-\r
- /**\r
- * Converts a string of digits to an double\r
- * @param s a string\r
- */\r
-\r
- public static double atof(String s) {\r
- int i = 0;\r
- int sign = 1;\r
- double r = 0; // integer part\r
- double f = 0; // fractional part\r
- double p = 1; // exponent of fractional part\r
- int state = 0; // 0 = int part, 1 = frac part\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '-') {\r
- sign = -1;\r
- i++;\r
- } else if (i < s.length() && s.charAt(i) == '+') {\r
- i++;\r
- }\r
- while (i < s.length()) {\r
- char ch = s.charAt(i);\r
- if ('0' <= ch && ch <= '9') {\r
- if (state == 0)\r
- r = r * 10 + ch - '0';\r
- else if (state == 1) {\r
- p = p / 10;\r
- r = r + p * (ch - '0');\r
- }\r
- } else if (ch == '.') {\r
- if (state == 0)\r
- state = 1;\r
- else\r
- return sign * r;\r
- } else if (ch == 'e' || ch == 'E') {\r
- long e = (int)parseLong(s.substring(i + 1), 10);\r
- return sign * r * Math.pow(10, e);\r
- } else\r
- return sign * r;\r
- i++;\r
- }\r
- return sign * r;\r
- }\r
-\r
- /**\r
- * Formats a double into a string (like sprintf in C)\r
- * @param x the number to format\r
- * @return the formatted string \r
- * @exception IllegalArgumentException if bad argument\r
- */\r
-\r
- public String form(double x) {\r
- String r;\r
- if (precision < 0)\r
- precision = 6;\r
- int s = 1;\r
- if (x < 0) {\r
- x = -x;\r
- s = -1;\r
- }\r
- if (fmt == 'f')\r
- r = fixed_format(x);\r
- else if (fmt == 'e' || fmt == 'E' || fmt == 'g' || fmt == 'G')\r
- r = exp_format(x);\r
- else\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- return pad(sign(s, r));\r
- }\r
-\r
- /**\r
- * Formats a long integer into a string (like sprintf in C)\r
- * @param x the number to format\r
- * @return the formatted string \r
- */\r
-\r
- public String form(long x) {\r
- String r;\r
- int s = 0;\r
- if (fmt == 'd' || fmt == 'i') {\r
- if (x < 0) {\r
- r = ("" + x).substring(1);\r
- s = -1;\r
- } else {\r
- r = "" + x;\r
- s = 1;\r
- }\r
- } else if (fmt == 'o')\r
- r = convert(x, 3, 7, "01234567");\r
- else if (fmt == 'x')\r
- r = convert(x, 4, 15, "0123456789abcdef");\r
- else if (fmt == 'X')\r
- r = convert(x, 4, 15, "0123456789ABCDEF");\r
- else\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- return pad(sign(s, r));\r
- }\r
-\r
- /**\r
- * Formats a character into a string (like sprintf in C)\r
- * @param x the value to format\r
- * @return the formatted string \r
- */\r
-\r
- public String form(char c) {\r
- if (fmt != 'c')\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- String r = "" + c;\r
- return pad(r);\r
- }\r
-\r
- /**\r
- * Formats a string into a larger string (like sprintf in C)\r
- * @param x the value to format\r
- * @return the formatted string \r
- */\r
-\r
- public String form(String s) {\r
- if (fmt != 's')\r
- throw new java.lang.IllegalArgumentException();\r
- if (precision >= 0)\r
- s = s.substring(0, precision);\r
- return pad(s);\r
- }\r
-\r
-\r
- /**\r
- * a test stub for the format class\r
- */\r
-\r
- public static void main(String[] a) {\r
- double x = 1.23456789012;\r
- double y = 123;\r
- double z = 1.2345e30;\r
- double w = 1.02;\r
- double u = 1.234e-5;\r
- int d = 0xCAFE;\r
- Format.print(System.out, "x = |%f|\n", x);\r
- Format.print(System.out, "u = |%20f|\n", u);\r
- Format.print(System.out, "x = |% .5f|\n", x);\r
- Format.print(System.out, "w = |%20.5f|\n", w);\r
- Format.print(System.out, "x = |%020.5f|\n", x);\r
- Format.print(System.out, "x = |%+20.5f|\n", x);\r
- Format.print(System.out, "x = |%+020.5f|\n", x);\r
- Format.print(System.out, "x = |% 020.5f|\n", x);\r
- Format.print(System.out, "y = |%#+20.5f|\n", y);\r
- Format.print(System.out, "y = |%-+20.5f|\n", y);\r
- Format.print(System.out, "z = |%20.5f|\n", z);\r
-\r
- Format.print(System.out, "x = |%e|\n", x);\r
- Format.print(System.out, "u = |%20e|\n", u);\r
- Format.print(System.out, "x = |% .5e|\n", x);\r
- Format.print(System.out, "w = |%20.5e|\n", w);\r
- Format.print(System.out, "x = |%020.5e|\n", x);\r
- Format.print(System.out, "x = |%+20.5e|\n", x);\r
- Format.print(System.out, "x = |%+020.5e|\n", x);\r
- Format.print(System.out, "x = |% 020.5e|\n", x);\r
- Format.print(System.out, "y = |%#+20.5e|\n", y);\r
- Format.print(System.out, "y = |%-+20.5e|\n", y);\r
-\r
- Format.print(System.out, "x = |%g|\n", x);\r
- Format.print(System.out, "z = |%g|\n", z);\r
- Format.print(System.out, "w = |%g|\n", w);\r
- Format.print(System.out, "u = |%g|\n", u);\r
- Format.print(System.out, "y = |%.2g|\n", y);\r
- Format.print(System.out, "y = |%#.2g|\n", y);\r
-\r
- Format.print(System.out, "d = |%d|\n", d);\r
- Format.print(System.out, "d = |%20d|\n", d);\r
- Format.print(System.out, "d = |%020d|\n", d);\r
- Format.print(System.out, "d = |%+20d|\n", d);\r
- Format.print(System.out, "d = |% 020d|\n", d);\r
- Format.print(System.out, "d = |%-20d|\n", d);\r
- Format.print(System.out, "d = |%20.8d|\n", d);\r
- Format.print(System.out, "d = |%x|\n", d);\r
- Format.print(System.out, "d = |%20X|\n", d);\r
- Format.print(System.out, "d = |%#20x|\n", d);\r
- Format.print(System.out, "d = |%020X|\n", d);\r
- Format.print(System.out, "d = |%20.8x|\n", d);\r
- Format.print(System.out, "d = |%o|\n", d);\r
- Format.print(System.out, "d = |%020o|\n", d);\r
- Format.print(System.out, "d = |%#20o|\n", d);\r
- Format.print(System.out, "d = |%#020o|\n", d);\r
- Format.print(System.out, "d = |%20.12o|\n", d);\r
-\r
- Format.print(System.out, "s = |%-20s|\n", "Hello");\r
- Format.print(System.out, "s = |%-20c|\n", '!');\r
-\r
- // regression test to confirm fix of reported bugs\r
-\r
- Format.print(System.out, "|%i|\n", Long.MIN_VALUE);\r
-\r
- Format.print(System.out, "|%6.2e|\n", 0.0);\r
- Format.print(System.out, "|%6.2g|\n", 0.0);\r
-\r
- Format.print(System.out, "|%6.2f|\n", 9.99);\r
- Format.print(System.out, "|%6.2f|\n", 9.999);\r
-\r
- Format.print(System.out, "|%6.0f|\n", 9.999);\r
- }\r
-\r
- private static String repeat(char c, int n) {\r
- if (n <= 0)\r
- return "";\r
- StringBuffer s = new StringBuffer(n);\r
- for (int i = 0; i < n; i++)\r
- s.append(c);\r
- return s.toString();\r
- }\r
-\r
- private static String convert(long x, int n, int m, String d) {\r
- if (x == 0)\r
- return "0";\r
- String r = "";\r
- while (x != 0) {\r
- r = d.charAt((int)(x & m)) + r;\r
- x = x >>> n;\r
- }\r
- return r;\r
- }\r
-\r
- private String pad(String r) {\r
- String p = repeat(' ', width - r.length());\r
- if (left_align)\r
- return pre + r + p + post;\r
- else\r
- return pre + p + r + post;\r
- }\r
-\r
- private String sign(int s, String r) {\r
- String p = "";\r
- if (s < 0)\r
- p = "-";\r
- else if (s > 0) {\r
- if (show_plus)\r
- p = "+";\r
- else if (show_space)\r
- p = " ";\r
- } else {\r
- if (fmt == 'o' && alternate && r.length() > 0 && r.charAt(0) != '0')\r
- p = "0";\r
- else if (fmt == 'x' && alternate)\r
- p = "0x";\r
- else if (fmt == 'X' && alternate)\r
- p = "0X";\r
- }\r
- int w = 0;\r
- if (leading_zeroes)\r
- w = width;\r
- else if ((fmt == 'd' || fmt == 'i' || fmt == 'x' || fmt == 'X' || fmt == 'o')\r
- && precision > 0)\r
- w = precision;\r
-\r
- return p + repeat('0', w - p.length() - r.length()) + r;\r
- }\r
-\r
- private String fixed_format(double d) {\r
- boolean removeTrailing\r
- = (fmt == 'G' || fmt == 'g') && !alternate;\r
- // remove trailing zeroes and decimal point\r
-\r
- if (d > 0x7FFFFFFFFFFFFFFFL)\r
- return exp_format(d);\r
- if (precision == 0)\r
- return (long)(d + 0.5) + (removeTrailing ? "" : ".");\r
-\r
- long whole = (long)d;\r
- double fr = d - whole; // fractional part\r
- if (fr >= 1 || fr < 0)\r
- return exp_format(d);\r
-\r
- double factor = 1;\r
- String leading_zeroes = "";\r
- for (int i = 1; i <= precision && factor <= 0x7FFFFFFFFFFFFFFFL; i++) {\r
- factor *= 10;\r
- leading_zeroes = leading_zeroes + "0";\r
- }\r
- long l = (long) (factor * fr + 0.5);\r
- if (l >= factor) {\r
- l = 0;\r
- whole++;\r
- } // CSH 10-25-97\r
-\r
- String z = leading_zeroes + l;\r
- z = "." + z.substring(z.length() - precision, z.length());\r
-\r
- if (removeTrailing) {\r
- int t = z.length() - 1;\r
- while (t >= 0 && z.charAt(t) == '0')\r
- t--;\r
- if (t >= 0 && z.charAt(t) == '.')\r
- t--;\r
- z = z.substring(0, t + 1);\r
- }\r
-\r
- return whole + z;\r
- }\r
-\r
- private String exp_format(double d) {\r
- String f = "";\r
- int e = 0;\r
- double dd = d;\r
- double factor = 1;\r
- if (d != 0) {\r
- while (dd > 10) {\r
- e++;\r
- factor /= 10;\r
- dd = dd / 10;\r
- }\r
- while (dd < 1) {\r
- e--;\r
- factor *= 10;\r
- dd = dd * 10;\r
- }\r
- }\r
- if ((fmt == 'g' || fmt == 'G') && e >= -4 && e < precision)\r
- return fixed_format(d);\r
-\r
- d = d * factor;\r
- f = f + fixed_format(d);\r
-\r
- if (fmt == 'e' || fmt == 'g')\r
- f = f + "e";\r
- else\r
- f = f + "E";\r
-\r
- String p = "000";\r
- if (e >= 0) {\r
- f = f + "+";\r
- p = p + e;\r
- } else {\r
- f = f + "-";\r
- p = p + (-e);\r
- }\r
-\r
- return f + p.substring(p.length() - 3, p.length());\r
- }\r
-\r
- private int width;\r
- private int precision;\r
- private String pre;\r
- private String post;\r
- private boolean leading_zeroes;\r
- private boolean show_plus;\r
- private boolean alternate;\r
- private boolean show_space;\r
- private boolean left_align;\r
- private char fmt; // one of cdeEfgGiosxXos\r
-}\r
-\r
-\r
-\r
-\r
-\r
+++ /dev/null
-package org.vamsas.objects.utils;\r
-\r
-/**\r
- * dict attribute values for glyph symbol sets found in uk.ac.vamsas.objects.core.AnnotationElement\r
- * TODO: add validators and multilength symbols.\r
- * @author JimP\r
- *\r
- */\r
-public class GlyphDictionary {\r
- /**\r
- * standard H, E, or C three state secondary structure assignment.\r
- */\r
- static final public String PROTEIN_SS_3STATE="aasecstr_3"; // HE, blank or C\r
- /**\r
- * default glyph type attribute indicates a UTF8 character\r
- */\r
- static final public String DEFAULT="utf8";\r
- /**\r
- * kyte and doolittle hydrophobicity\r
- * TODO: specify this glyph set.\r
- */\r
- static final public String PROTEIN_HD_HYDRO="kd_hydrophobicity";\r
-}\r
+++ /dev/null
-package org.vamsas.objects.utils;
-
-import java.util.Date;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.Provenance;
-
-public class ProvenanceStuff {
-
- /**
- * stuff for making and doing things with provenance objects.
- */
- static Log log = LogFactory.getLog(ProvenanceStuff.class);
-
- /**
- * @param app TODO
- * @param action
- * text for action entry
- * @return new Provenance entry for ArchiveWriter created docs.
- * TODO: Verify and move to SimpleClient class for provenance handling
- */
- public static Entry newProvenanceEntry(String app, String user, String action) {
- log.debug("Adding ProvenanceEntry("+user+","+action+")");
- Entry e = new Entry();
- e.setApp(app);
- e.setAction(action);
- e.setUser(user);
- e.setDate(new org.exolab.castor.types.Date(new Date()));
- return e;
- }
- public static Provenance newProvenance(Entry entry) {
- Provenance list = new Provenance();
- list.addEntry(entry);
- return list;
- }
- public static Provenance newProvenance(String user, String action) {
- return newProvenance(ProvenanceStuff.newProvenanceEntry("vamsasApp:ExampleVamsasClient/alpha", user, action));
- }
- public static Provenance newProvenance(String app, String user, String action) {
- return newProvenance(ProvenanceStuff.newProvenanceEntry(app, user, action));
- }
-
-}
+++ /dev/null
-/*
- * Created on 17-May-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.objects.utils;
-
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.util.regex.Pattern;
-
-import uk.ac.vamsas.objects.core.AlignmentSequence;
-import uk.ac.vamsas.objects.core.Sequence;
-import uk.ac.vamsas.objects.core.SequenceType;
-
-/**
- * @author jimp
- *
- * TODO To change the template for this generated type comment go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-public class Seq {
-
- public static void write_PirSeq(OutputStream os, SequenceType seq, int wid) throws IOException {
- BufferedWriter pir_out = new BufferedWriter(new OutputStreamWriter(os));
- pir_out.write(">P1;"+seq.getName()+"\n");
- int width = (wid<1) ? 80 : wid;
- for (int j=0,k=seq.getSequence().length(); j<k; j+=width)
- if (j+width<k)
- pir_out.write(seq.getSequence().substring(j,j+width)+"\n");
- else
- pir_out.write(seq.getSequence().substring(j)+"\n");
- pir_out.flush();
- }
-
- public static void write_FastaSeq(OutputStream os, SequenceType seq) throws IOException {
- BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
- fasta_out.write(">"+seq.getName()+"\n");
- fasta_out.write(seq.getSequence()+"\n");
- fasta_out.flush();
- }
-
- public static void write_FastaSeq(OutputStream os, SequenceType seq, int wid) throws IOException {
- BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
- fasta_out.write(">"+seq.getName()+"\n");
- int width = (wid<1) ? 80 : wid;
- for (int j=0,k=seq.getSequence().length(); j<k; j+=width)
- if (j+width<k)
- fasta_out.write(seq.getSequence().substring(j,j+width)+"\n");
- else
- fasta_out.write(seq.getSequence().substring(j)+"\n");
- fasta_out.flush();
- }
- /**
- *validate a SequenceType Vobject as an info:iubmb.org/aminoacid SequenceType
- *This version resolves references to Sequence objects from AlignmentSequence
- *TODO: Define info: urn for dictionary string (could also be regex of valid characters!)
- * @param s
- * @param dict TODO
- * @return true if a valid amino acid sequence Vobject
- */
- private static boolean valid_aadictionary_string(String s, String dict) {
- if (s==null)
- return false;
- // validate against dictionary
- // TODO generalise to resolve dictionary against info: urn for dictionary type
- Pattern aa_repl = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUX]+", Pattern.CASE_INSENSITIVE);
- String remnants = aa_repl.matcher(s).replaceAll("");
- return !remnants.matches("//S+");
- }
-
- public static Sequence newSequence(String Name, String Sequence, String Dictionary, int start, int end) {
- //TODO: make hierarchy reflecting the SeqType Vobject.
- Sequence seq= new Sequence();
- seq.setDictionary(Dictionary);
- seq.setName(Name);
- seq.setSequence(Sequence);
- seq.setStart(start);
- if (start<=end) {
- if ((end-start)!=Sequence.length())
- seq.setEnd(start+Sequence.length());
- } else {
- // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence Vobject
- if ((start-end)!=Sequence.length())
- seq.setEnd(end+Sequence.length());
- }
- return seq;
- }
- public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, int start, int end) {
- if (refseq!=null) {
- AlignmentSequence asq = new AlignmentSequence();
- asq.setName(name);
- asq.setSequence(alSequence);
- asq.setRefid(refseq);
- if (start<refseq.getStart())
- start = refseq.getStart();
- asq.setStart(start);
- if (end>refseq.getEnd())
- end = refseq.getEnd();
- asq.setEnd(end);
- return asq;
- }
- return null;
- }
- public static boolean is_valid_aa_seq(SequenceType s) {
- Sequence q;
- boolean validref=false;
- if (s instanceof Sequence) {
- q=(Sequence) s;
- if (q.getDictionary()!=null
-
- && q.getDictionary().length()>0
- || !q.getDictionary().equals(SymbolDictionary.STANDARD_AA))
- return false;
- return valid_aadictionary_string(q.getSequence(), SymbolDictionary.STANDARD_AA);
- }
-
- // follow references
- if (s instanceof AlignmentSequence) {
- Object w = (((AlignmentSequence) s).getRefid());
- if (w!=null && w!=s && w instanceof SequenceType)
- return is_valid_aa_seq((SequenceType) w)
- && valid_aadictionary_string(((AlignmentSequence) s).getSequence(), SymbolDictionary.STANDARD_AA);
- }
-
- return false;
- }
-}
+++ /dev/null
-/*
- * Created on 17-May-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.objects.utils;
-
-import java.io.BufferedOutputStream;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-import java.util.Vector;
-import java.util.regex.Pattern;
-
-import uk.ac.vamsas.objects.core.*;
-
-/**
- * @author jimp
- *
- * TODO To change the template for this generated type comment go to Window -
- * Preferences - Java - Code Style - Code Templates
- */
-public class SeqAln extends uk.ac.vamsas.objects.core.Alignment {
-
- public static Sequence[] ReadClustalFile(InputStream os) throws Exception {
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- Pattern nonGap = Pattern.compile("[A-Z*0-9]", Pattern.CASE_INSENSITIVE);
- String gapchars = "";
- char gapchar = '-';
-
- int i = 0;
- boolean flag = false;
-
- Vector headers = new Vector();
- Hashtable seqhash = new Hashtable();
- Sequence[] seqs = null;
- int noSeqs = 0;
- String line;
-
- try {
- BufferedReader ins = new BufferedReader(new InputStreamReader(os));
- while ((line = ins.readLine()) != null) {
- if (line.indexOf(" ") != 0) {
- java.util.StringTokenizer str = new StringTokenizer(line, " ");
- String id = "";
-
- if (str.hasMoreTokens()) {
- id = str.nextToken();
- if (id.equals("CLUSTAL")) {
- flag = true;
- } else {
- if (flag) {
- StringBuffer tempseq;
- if (seqhash.containsKey(id)) {
- tempseq = (StringBuffer) seqhash.get(id);
- } else {
- tempseq = new StringBuffer();
- seqhash.put(id, tempseq);
- }
-
- if (!(headers.contains(id))) {
- headers.addElement(id);
- }
-
- tempseq.append(str.nextToken());
- }
- }
- }
- }
- }
-
- } catch (IOException e) {
- throw (new Exception("Exception parsing clustal file ", e));
- }
-
- if (flag) {
- noSeqs = headers.size();
-
- // Add sequences to the hash
- seqs = new Sequence[headers.size()];
- for (i = 0; i < headers.size(); i++) {
- if (seqhash.get(headers.elementAt(i)) != null) {
- // TODO: develop automatic dictionary typing for sequences
- Sequence newSeq = Seq.newSequence(headers.elementAt(i).toString(),
- seqhash.get(headers.elementAt(i).toString()).toString(),
- SymbolDictionary.STANDARD_AA,0,0);
-
- seqs[i] = newSeq;
-
- } else {
- throw (new Exception("Bizarreness! Can't find sequence for "
- + headers.elementAt(i)));
- }
- }
- }
- return seqs;
- }
-
- public static void WriteClustalWAlignment(java.io.OutputStream os,
- Alignment seqAl) throws IOException {
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- AlignmentSequence[] s = seqAl.getAlignmentSequence();
-
- java.io.BufferedWriter out = new BufferedWriter(
- new java.io.OutputStreamWriter(os));
-
- out.write("CLUSTAL\n\n");
-
- int max = 0;
- int maxid = 0;
-
- int i = 0;
-
- while (i < s.length && s[i] != null) {
- String tmp = s[i].getId();
-
- if (s[i].getSequence().length() > max) {
- max = s[i].getSequence().length();
- }
- if (tmp.length() > maxid) {
- maxid = tmp.length();
- }
- i++;
- }
-
- if (maxid < 15) {
- maxid = 15;
- }
- maxid++;
- int len = 60;
- int nochunks = max / len + 1;
-
- for (i = 0; i < nochunks; i++) {
- int j = 0;
- while (j < s.length && s[j] != null) {
- out.write(new Format("%-" + maxid + "s").form(s[j].getId() + " "));
- int start = i * len;
- int end = start + len;
-
- if (end < s[j].getSequence().length() && start < s[j].getSequence().length()) {
- out.write(s[j].getSequence().substring(start, end) + "\n");
- } else {
- if (start < s[j].getSequence().length()) {
- out.write(s[j].getSequence().substring(start) + "\n");
- }
- }
- j++;
- }
- out.write("\n");
-
- }
- }
- /**
- * manufacture an alignment/dataset from an array of sequences
- * @param origin
- * @param seqs
- * @return
- * @throws Exception
- */
- public static Alignment make_Alignment(Entry origin,
- Sequence[] seqs) throws Exception {
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- Alignment al = new Alignment();
- al.setProvenance(ProvenanceStuff.newProvenance(origin));
-
- Pattern nonGap = Pattern.compile("[A-Z*0-9]", Pattern.CASE_INSENSITIVE);
- boolean gapsset = false;
- char gapchar = '-';
- int seqLength = 0;
-
- for (int i = 0, nseq = seqs.length; i < nseq; i++) {
- String seq = seqs[i].getSequence();
- String gaps = nonGap.matcher(seq).replaceAll("");
- if (seqLength == 0) {
- seqLength = seq.length();
- } else if (seqLength != seq.length())
- throw (new Exception(i + "th Sequence (>" + seqs[i].getId()
- + ") is not aligned.\n"));// TODO: move this to assertions part of
- // Alignment
-
- // common check for any sequence...
- if (gaps != null && gaps.length() > 0) {
- if (!gapsset)
- gapchar = gaps.charAt(0);
- for (int c = 0, gc = gaps.length(); c < gc; c++) {
- if (gapchar != gaps.charAt(c)) {
- throw (new IOException("Inconsistent gap characters in sequence "
- + i + ": '" + seq + "'"));
- }
- }
- }
- AlignmentSequence sq = new AlignmentSequence();
- // TODO: use as basis of default AlignSequence(Sequence) constructor.
- sq.setSequence(seq);
- sq.setName(seqs[i].getId());
- sq.setRefid(seqs[i].getVorbaId());
- sq.setStart(seqs[i].getStart());
- sq.setEnd(seqs[i].getEnd());
- al.addAlignmentSequence(sq);
- }
- al.setGapChar(String.valueOf(gapchar));
- return al;
- }
-
- public static Alignment read_FastaAlignment(InputStream os, Entry entry)
- throws Exception {
- Sequence[] seqs;
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- try {
- seqs = SeqSet.read_SeqFasta(os);
- if (seqs == null)
- throw (new Exception("Empty alignment stream!\n"));
- } catch (Exception e) {
- throw new Exception("Invalid fasta alignment\n", e);
- }
-
- return make_Alignment(entry, seqs);
- }
-
- public static Alignment read_ClustalAlignment(InputStream os, Entry entry)
- throws Exception {
- Sequence[] seqs;
- try {
- seqs = SeqAln.ReadClustalFile(os);
- if (seqs == null)
- throw (new Exception("Empty alignment stream!\n"));
- } catch (Exception e) {
- throw new Exception("Invalid fasta alignment\n", e);
- }
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- return make_Alignment(entry, seqs);
- }
-}
+++ /dev/null
-/*
- * Created on 17-May-2005
- * Slurped into VamsasClient object set on 12th Jan 2006
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.objects.utils;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.util.Hashtable;
-import java.util.Vector;
-import java.util.regex.Pattern;
-
-import uk.ac.vamsas.objects.core.*;
-
-/**
- * @author jimp
- *
- * TODO To change the template for this generated type comment go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-public class SeqSet {
-
- public static void write_Fasta(OutputStream os, SequenceType[] seqs) throws IOException {
- write_Fasta(os, seqs, 80);
- }
-
- public static void write_Fasta(OutputStream os, SequenceType[] seqs, boolean width80) throws IOException {
- write_Fasta(os, seqs, (width80) ? 80 : 0);
- }
-
- public static void write_Fasta(OutputStream os, SequenceType[] seqs, int width) throws IOException {
- int i, nseq = seqs.length;
- BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- for (i=0; i<nseq; i++) {
- fasta_out.write(">"+seqs[i].getName()+"\n");
- if (width<=0) {
- fasta_out.write(seqs[i].getSequence()+"\n");
- } else {
- // TODO: adapt to SymbolDictionary labelwidths
- String tempseq = seqs[i].getSequence();
- int j=0, k=tempseq.length();
- while (j<k) {
- int d = k-j;
- if (d>=width) {
- fasta_out.write(tempseq, j, width);
- } else {
- fasta_out.write(tempseq, j, d);
- }
- fasta_out.write("\n");
- j+=width;
- }
- }
- }
- fasta_out.flush();
- }
- /**
- * TODO: introduce a dictionary parameter for qualified sequence symbols
- * Reads a sequence set from a stream - will only read prescribed amino acid
- * symbols.
- * @param os
- * @return
- * @throws IOException
- */
- public static Sequence[] read_SeqFasta(InputStream os) throws IOException {
- Vector seqs = new Vector();
- int nseq = 0;
- BufferedReader infasta = new BufferedReader(new InputStreamReader(os));
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- // TODO: decide on return type - SequenceType is a partly complete vamsas Vobject - either for a dataset or alignment sequence
- // so could go in either!
- String line;
- Sequence seq = null;
- Pattern aaMatch = Pattern.compile("[ARNDCQEGHILKMFPSTUWYV]", Pattern.CASE_INSENSITIVE);
- String sname = "", seqstr=null;
- do {
- line = infasta.readLine();
- if (line==null || line.startsWith(">")) {
- if (seqstr!=null)
- seqs.add((Object) Seq.newSequence(sname.substring(1), seqstr, SymbolDictionary.STANDARD_AA, 0,0));
- sname = line; // remove >
- seqstr="";
- } else {
- String subseq = Pattern.compile("//s+").matcher(line).replaceAll("");
- seqstr += subseq;
- }
- } while (line!=null);
- nseq = seqs.size();
- if (nseq>0) {
- // TODO:POSS: should really return a sequence if there's only one in the file.
- Sequence[] seqset = new Sequence[nseq];
- for (int i=0; i<nseq; i++) {
- seqset[i] = (Sequence) seqs.elementAt(i);
- }
- return seqset;
- }
-
- return null;
- }
-
- public static Hashtable uniquify(SequenceType[] sequences) {
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- // TODO: do we need this with vamsas sequences ?
- // Generate a safely named sequence set and a hash to recover the sequence names
- Hashtable map = new Hashtable();
- for (int i = 0; i < sequences.length; i++) {
- String safename = new String("Sequence" + i);
- map.put(safename, sequences[i].getName());
- sequences[i].setName(safename);
- }
- return map;
- }
-
- public static boolean deuniquify(Hashtable map, SequenceType[] sequences) {
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- // TODO: do we need this with vamsas sequences ?
- // recover unsafe sequence names for a sequence set
- boolean allfound = true;
- for (int i = 0; i < sequences.length; i++) {
- if (map.containsKey(sequences[i].getName())) {
- String unsafename = (String) map.get(sequences[i].getName());
- sequences[i].setName(unsafename);
- } else {
- allfound = false;
- }
- }
- return allfound;
- }
-
-}
+++ /dev/null
-package org.vamsas.objects.utils;
-
-public class SymbolDictionary {
- /**
- * defines standard names and properties for vamsas sequence dictionaries
- */
- static final public String STANDARD_AA="info:iubmb.org/aminoacids"; // strict 1 letter code
- static final public String STANDARD_NA="info:iubmb.org/nucleosides";// strict 1 letter code (do not allow arbitrary rare nucleosides)
- /**
- * TODO: Vamsas Dictionary properties interface
- * an interface for dictionary provides :
- * validation for a string
- * symbolwidth (or symbol next/previous)
- * mappings to certain other dictionaries (one2three, etc)
- * gap-character test
- *
- */
-
-}
git://source.jalview.org / vamsas.git / commitdiff