From 3539a744220b536baa07a1030bf1a3d2e36226b7 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 14 Dec 2006 18:20:51 +0000 Subject: [PATCH] refactoring org to uk git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@280 be28352e-c001-0410-b1a7-c7978e42abec --- src/org/vamsas/objects/utils/AppDataReference.java | 161 ----- src/org/vamsas/objects/utils/DocumentStuff.java | 35 -- src/org/vamsas/objects/utils/Format.java | 612 -------------------- src/org/vamsas/objects/utils/GlyphDictionary.java | 23 - src/org/vamsas/objects/utils/ProvenanceStuff.java | 46 -- src/org/vamsas/objects/utils/Seq.java | 131 ----- src/org/vamsas/objects/utils/SeqAln.java | 238 -------- src/org/vamsas/objects/utils/SeqSet.java | 138 ----- src/org/vamsas/objects/utils/SymbolDictionary.java | 19 - 9 files changed, 1403 deletions(-) delete mode 100644 src/org/vamsas/objects/utils/AppDataReference.java delete mode 100644 src/org/vamsas/objects/utils/DocumentStuff.java delete mode 100644 src/org/vamsas/objects/utils/Format.java delete mode 100644 src/org/vamsas/objects/utils/GlyphDictionary.java delete mode 100644 src/org/vamsas/objects/utils/ProvenanceStuff.java delete mode 100644 src/org/vamsas/objects/utils/Seq.java delete mode 100644 src/org/vamsas/objects/utils/SeqAln.java delete mode 100644 src/org/vamsas/objects/utils/SeqSet.java delete mode 100644 src/org/vamsas/objects/utils/SymbolDictionary.java diff --git a/src/org/vamsas/objects/utils/AppDataReference.java b/src/org/vamsas/objects/utils/AppDataReference.java deleted file mode 100644 index c0e8109..0000000 --- a/src/org/vamsas/objects/utils/AppDataReference.java +++ /dev/null @@ -1,161 +0,0 @@ -/** - * - */ -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; q0) - 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; q0) - 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 - *
  • a % (required) - *
  • a modifier (optional) - *
    - *
    +
    forces display of + for positive numbers - *
    0
    show leading zeroes - *
    -
    align left in the field - *
    space
    prepend a space in front of positive numbers - *
    #
    use "alternate" format. Add 0 or 0x for octal or hexadecimal numbers. Don't suppress trailing zeroes in general floating point format. - *
    - *
  • an integer denoting field width (optional) - *
  • a period followed by an integer denoting precision (optional) - *
  • a format descriptor (required) - *
    - *
    f
    floating point number in fixed format - *
    e, E
    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. - *
    g, G
    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. - *
    d, i
    integer in decimal - *
    x
    integer in hexadecimal - *
    o
    integer in octal - *
    s
    string - *
    c
    character - *
    - * - * @exception IllegalArgumentException if bad format - */ - - public Format(String s) { - width = 0; - precision = -1; - pre = ""; - post = ""; - leading_zeroes = false; - show_plus = false; - alternate = false; - show_space = false; - left_align = false; - fmt = ' '; - - int state = 0; - int length = s.length(); - int parse_state = 0; - // 0 = prefix, 1 = flags, 2 = width, 3 = precision, - // 4 = format, 5 = end - int i = 0; - - while (parse_state == 0) { - if (i >= length) - parse_state = 5; - else if (s.charAt(i) == '%') { - if (i < length - 1) { - if (s.charAt(i + 1) == '%') { - pre = pre + '%'; - i++; - } else - parse_state = 1; - } else - throw new java.lang.IllegalArgumentException(); - } else - pre = pre + s.charAt(i); - i++; - } - while (parse_state == 1) { - if (i >= length) - parse_state = 5; - else if (s.charAt(i) == ' ') - show_space = true; - else if (s.charAt(i) == '-') - left_align = true; - else if (s.charAt(i) == '+') - show_plus = true; - else if (s.charAt(i) == '0') - leading_zeroes = true; - else if (s.charAt(i) == '#') - alternate = true; - else { - parse_state = 2; - i--; - } - i++; - } - while (parse_state == 2) { - if (i >= length) - parse_state = 5; - else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') { - width = width * 10 + s.charAt(i) - '0'; - i++; - } else if (s.charAt(i) == '.') { - parse_state = 3; - precision = 0; - i++; - } else - parse_state = 4; - } - while (parse_state == 3) { - if (i >= length) - parse_state = 5; - else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') { - precision = precision * 10 + s.charAt(i) - '0'; - i++; - } else - parse_state = 4; - } - if (parse_state == 4) { - if (i >= length) - parse_state = 5; - else - fmt = s.charAt(i); - i++; - } - if (i < length) - post = s.substring(i, length); - } - - /** - * prints a formatted number following printf conventions - * @param s a PrintStream - * @param fmt the format string - * @param x the double to print - */ - - public static void print(java.io.PrintStream s, String fmt, double x) { - s.print(new Format(fmt).form(x)); - } - - /** - * prints a formatted number following printf conventions - * @param s a PrintStream - * @param fmt the format string - * @param x the long to print - */ - public static void print(java.io.PrintStream s, String fmt, long x) { - s.print(new Format(fmt).form(x)); - } - - /** - * prints a formatted number following printf conventions - * @param s a PrintStream - * @param fmt the format string - * @param x the character to - */ - - public static void print(java.io.PrintStream s, String fmt, char x) { - s.print(new Format(fmt).form(x)); - } - - /** - * prints a formatted number following printf conventions - * @param s a PrintStream, fmt the format string - * @param x a string that represents the digits to print - */ - - public static void print(java.io.PrintStream s, String fmt, String x) { - s.print(new Format(fmt).form(x)); - } - - /** - * Converts a string of digits (decimal, octal or hex) to an integer - * @param s a string - * @return the numeric value of the prefix of s representing a base 10 integer - */ - - public static int atoi(String s) { - return (int)atol(s); - } - - /** - * Converts a string of digits (decimal, octal or hex) to a long integer - * @param s a string - * @return the numeric value of the prefix of s representing a base 10 integer - */ - - public static long atol(String s) { - int i = 0; - - while (i < s.length() && Character.isWhitespace(s.charAt(i))) - i++; - if (i < s.length() && s.charAt(i) == '0') { - if (i + 1 < s.length() && (s.charAt(i + 1) == 'x' || s.charAt(i + 1) == 'X')) - return parseLong(s.substring(i + 2), 16); - else - return parseLong(s, 8); - } else - return parseLong(s, 10); - } - - private static long parseLong(String s, int base) { - int i = 0; - int sign = 1; - long r = 0; - - while (i < s.length() && Character.isWhitespace(s.charAt(i))) - i++; - if (i < s.length() && s.charAt(i) == '-') { - sign = -1; - i++; - } else if (i < s.length() && s.charAt(i) == '+') { - i++; - } - while (i < s.length()) { - char ch = s.charAt(i); - if ('0' <= ch && ch < '0' + base) - r = r * base + ch - '0'; - else if ('A' <= ch && ch < 'A' + base - 10) - r = r * base + ch - 'A' + 10 ; - else if ('a' <= ch && ch < 'a' + base - 10) - r = r * base + ch - 'a' + 10 ; - else - return r * sign; - i++; - } - return r * sign; - } - - /** - * Converts a string of digits to an double - * @param s a string - */ - - public static double atof(String s) { - int i = 0; - int sign = 1; - double r = 0; // integer part - double f = 0; // fractional part - double p = 1; // exponent of fractional part - int state = 0; // 0 = int part, 1 = frac part - - while (i < s.length() && Character.isWhitespace(s.charAt(i))) - i++; - if (i < s.length() && s.charAt(i) == '-') { - sign = -1; - i++; - } else if (i < s.length() && s.charAt(i) == '+') { - i++; - } - while (i < s.length()) { - char ch = s.charAt(i); - if ('0' <= ch && ch <= '9') { - if (state == 0) - r = r * 10 + ch - '0'; - else if (state == 1) { - p = p / 10; - r = r + p * (ch - '0'); - } - } else if (ch == '.') { - if (state == 0) - state = 1; - else - return sign * r; - } else if (ch == 'e' || ch == 'E') { - long e = (int)parseLong(s.substring(i + 1), 10); - return sign * r * Math.pow(10, e); - } else - return sign * r; - i++; - } - return sign * r; - } - - /** - * Formats a double into a string (like sprintf in C) - * @param x the number to format - * @return the formatted string - * @exception IllegalArgumentException if bad argument - */ - - public String form(double x) { - String r; - if (precision < 0) - precision = 6; - int s = 1; - if (x < 0) { - x = -x; - s = -1; - } - if (fmt == 'f') - r = fixed_format(x); - else if (fmt == 'e' || fmt == 'E' || fmt == 'g' || fmt == 'G') - r = exp_format(x); - else - throw new java.lang.IllegalArgumentException(); - - return pad(sign(s, r)); - } - - /** - * Formats a long integer into a string (like sprintf in C) - * @param x the number to format - * @return the formatted string - */ - - public String form(long x) { - String r; - int s = 0; - if (fmt == 'd' || fmt == 'i') { - if (x < 0) { - r = ("" + x).substring(1); - s = -1; - } else { - r = "" + x; - s = 1; - } - } else if (fmt == 'o') - r = convert(x, 3, 7, "01234567"); - else if (fmt == 'x') - r = convert(x, 4, 15, "0123456789abcdef"); - else if (fmt == 'X') - r = convert(x, 4, 15, "0123456789ABCDEF"); - else - throw new java.lang.IllegalArgumentException(); - - return pad(sign(s, r)); - } - - /** - * Formats a character into a string (like sprintf in C) - * @param x the value to format - * @return the formatted string - */ - - public String form(char c) { - if (fmt != 'c') - throw new java.lang.IllegalArgumentException(); - - String r = "" + c; - return pad(r); - } - - /** - * Formats a string into a larger string (like sprintf in C) - * @param x the value to format - * @return the formatted string - */ - - public String form(String s) { - if (fmt != 's') - throw new java.lang.IllegalArgumentException(); - if (precision >= 0) - s = s.substring(0, precision); - return pad(s); - } - - - /** - * a test stub for the format class - */ - - public static void main(String[] a) { - double x = 1.23456789012; - double y = 123; - double z = 1.2345e30; - double w = 1.02; - double u = 1.234e-5; - int d = 0xCAFE; - Format.print(System.out, "x = |%f|\n", x); - Format.print(System.out, "u = |%20f|\n", u); - Format.print(System.out, "x = |% .5f|\n", x); - Format.print(System.out, "w = |%20.5f|\n", w); - Format.print(System.out, "x = |%020.5f|\n", x); - Format.print(System.out, "x = |%+20.5f|\n", x); - Format.print(System.out, "x = |%+020.5f|\n", x); - Format.print(System.out, "x = |% 020.5f|\n", x); - Format.print(System.out, "y = |%#+20.5f|\n", y); - Format.print(System.out, "y = |%-+20.5f|\n", y); - Format.print(System.out, "z = |%20.5f|\n", z); - - Format.print(System.out, "x = |%e|\n", x); - Format.print(System.out, "u = |%20e|\n", u); - Format.print(System.out, "x = |% .5e|\n", x); - Format.print(System.out, "w = |%20.5e|\n", w); - Format.print(System.out, "x = |%020.5e|\n", x); - Format.print(System.out, "x = |%+20.5e|\n", x); - Format.print(System.out, "x = |%+020.5e|\n", x); - Format.print(System.out, "x = |% 020.5e|\n", x); - Format.print(System.out, "y = |%#+20.5e|\n", y); - Format.print(System.out, "y = |%-+20.5e|\n", y); - - Format.print(System.out, "x = |%g|\n", x); - Format.print(System.out, "z = |%g|\n", z); - Format.print(System.out, "w = |%g|\n", w); - Format.print(System.out, "u = |%g|\n", u); - Format.print(System.out, "y = |%.2g|\n", y); - Format.print(System.out, "y = |%#.2g|\n", y); - - Format.print(System.out, "d = |%d|\n", d); - Format.print(System.out, "d = |%20d|\n", d); - Format.print(System.out, "d = |%020d|\n", d); - Format.print(System.out, "d = |%+20d|\n", d); - Format.print(System.out, "d = |% 020d|\n", d); - Format.print(System.out, "d = |%-20d|\n", d); - Format.print(System.out, "d = |%20.8d|\n", d); - Format.print(System.out, "d = |%x|\n", d); - Format.print(System.out, "d = |%20X|\n", d); - Format.print(System.out, "d = |%#20x|\n", d); - Format.print(System.out, "d = |%020X|\n", d); - Format.print(System.out, "d = |%20.8x|\n", d); - Format.print(System.out, "d = |%o|\n", d); - Format.print(System.out, "d = |%020o|\n", d); - Format.print(System.out, "d = |%#20o|\n", d); - Format.print(System.out, "d = |%#020o|\n", d); - Format.print(System.out, "d = |%20.12o|\n", d); - - Format.print(System.out, "s = |%-20s|\n", "Hello"); - Format.print(System.out, "s = |%-20c|\n", '!'); - - // regression test to confirm fix of reported bugs - - Format.print(System.out, "|%i|\n", Long.MIN_VALUE); - - Format.print(System.out, "|%6.2e|\n", 0.0); - Format.print(System.out, "|%6.2g|\n", 0.0); - - Format.print(System.out, "|%6.2f|\n", 9.99); - Format.print(System.out, "|%6.2f|\n", 9.999); - - Format.print(System.out, "|%6.0f|\n", 9.999); - } - - private static String repeat(char c, int n) { - if (n <= 0) - return ""; - StringBuffer s = new StringBuffer(n); - for (int i = 0; i < n; i++) - s.append(c); - return s.toString(); - } - - private static String convert(long x, int n, int m, String d) { - if (x == 0) - return "0"; - String r = ""; - while (x != 0) { - r = d.charAt((int)(x & m)) + r; - x = x >>> n; - } - return r; - } - - private String pad(String r) { - String p = repeat(' ', width - r.length()); - if (left_align) - return pre + r + p + post; - else - return pre + p + r + post; - } - - private String sign(int s, String r) { - String p = ""; - if (s < 0) - p = "-"; - else if (s > 0) { - if (show_plus) - p = "+"; - else if (show_space) - p = " "; - } else { - if (fmt == 'o' && alternate && r.length() > 0 && r.charAt(0) != '0') - p = "0"; - else if (fmt == 'x' && alternate) - p = "0x"; - else if (fmt == 'X' && alternate) - p = "0X"; - } - int w = 0; - if (leading_zeroes) - w = width; - else if ((fmt == 'd' || fmt == 'i' || fmt == 'x' || fmt == 'X' || fmt == 'o') - && precision > 0) - w = precision; - - return p + repeat('0', w - p.length() - r.length()) + r; - } - - private String fixed_format(double d) { - boolean removeTrailing - = (fmt == 'G' || fmt == 'g') && !alternate; - // remove trailing zeroes and decimal point - - if (d > 0x7FFFFFFFFFFFFFFFL) - return exp_format(d); - if (precision == 0) - return (long)(d + 0.5) + (removeTrailing ? "" : "."); - - long whole = (long)d; - double fr = d - whole; // fractional part - if (fr >= 1 || fr < 0) - return exp_format(d); - - double factor = 1; - String leading_zeroes = ""; - for (int i = 1; i <= precision && factor <= 0x7FFFFFFFFFFFFFFFL; i++) { - factor *= 10; - leading_zeroes = leading_zeroes + "0"; - } - long l = (long) (factor * fr + 0.5); - if (l >= factor) { - l = 0; - whole++; - } // CSH 10-25-97 - - String z = leading_zeroes + l; - z = "." + z.substring(z.length() - precision, z.length()); - - if (removeTrailing) { - int t = z.length() - 1; - while (t >= 0 && z.charAt(t) == '0') - t--; - if (t >= 0 && z.charAt(t) == '.') - t--; - z = z.substring(0, t + 1); - } - - return whole + z; - } - - private String exp_format(double d) { - String f = ""; - int e = 0; - double dd = d; - double factor = 1; - if (d != 0) { - while (dd > 10) { - e++; - factor /= 10; - dd = dd / 10; - } - while (dd < 1) { - e--; - factor *= 10; - dd = dd * 10; - } - } - if ((fmt == 'g' || fmt == 'G') && e >= -4 && e < precision) - return fixed_format(d); - - d = d * factor; - f = f + fixed_format(d); - - if (fmt == 'e' || fmt == 'g') - f = f + "e"; - else - f = f + "E"; - - String p = "000"; - if (e >= 0) { - f = f + "+"; - p = p + e; - } else { - f = f + "-"; - p = p + (-e); - } - - return f + p.substring(p.length() - 3, p.length()); - } - - private int width; - private int precision; - private String pre; - private String post; - private boolean leading_zeroes; - private boolean show_plus; - private boolean alternate; - private boolean show_space; - private boolean left_align; - private char fmt; // one of cdeEfgGiosxXos -} - - - - - diff --git a/src/org/vamsas/objects/utils/GlyphDictionary.java b/src/org/vamsas/objects/utils/GlyphDictionary.java deleted file mode 100644 index 88134bf..0000000 --- a/src/org/vamsas/objects/utils/GlyphDictionary.java +++ /dev/null @@ -1,23 +0,0 @@ -package org.vamsas.objects.utils; - -/** - * dict attribute values for glyph symbol sets found in uk.ac.vamsas.objects.core.AnnotationElement - * TODO: add validators and multilength symbols. - * @author JimP - * - */ -public class GlyphDictionary { - /** - * standard H, E, or C three state secondary structure assignment. - */ - static final public String PROTEIN_SS_3STATE="aasecstr_3"; // HE, blank or C - /** - * default glyph type attribute indicates a UTF8 character - */ - static final public String DEFAULT="utf8"; - /** - * kyte and doolittle hydrophobicity - * TODO: specify this glyph set. - */ - static final public String PROTEIN_HD_HYDRO="kd_hydrophobicity"; -} diff --git a/src/org/vamsas/objects/utils/ProvenanceStuff.java b/src/org/vamsas/objects/utils/ProvenanceStuff.java deleted file mode 100644 index 9d668d5..0000000 --- a/src/org/vamsas/objects/utils/ProvenanceStuff.java +++ /dev/null @@ -1,46 +0,0 @@ -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)); - } - -} diff --git a/src/org/vamsas/objects/utils/Seq.java b/src/org/vamsas/objects/utils/Seq.java deleted file mode 100644 index 7785050..0000000 --- a/src/org/vamsas/objects/utils/Seq.java +++ /dev/null @@ -1,131 +0,0 @@ -/* - * 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"+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(); jend 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 (startrefseq.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; - } -} diff --git a/src/org/vamsas/objects/utils/SeqAln.java b/src/org/vamsas/objects/utils/SeqAln.java deleted file mode 100644 index b76d8ce..0000000 --- a/src/org/vamsas/objects/utils/SeqAln.java +++ /dev/null @@ -1,238 +0,0 @@ -/* - * 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); - } -} diff --git a/src/org/vamsas/objects/utils/SeqSet.java b/src/org/vamsas/objects/utils/SeqSet.java deleted file mode 100644 index 88e5345..0000000 --- a/src/org/vamsas/objects/utils/SeqSet.java +++ /dev/null @@ -1,138 +0,0 @@ -/* - * 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"+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=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